Development of a multiplex real-time quantitative reverse-transcription polymerase chain reaction for the detection of four bee viruses.

Viruses in the families Dicistroviridae and Iflaviridae are among the main threats to western honey bees (Apis mellifera) and native bee species. Polymerase chain reaction (PCR) is the gold standard for pathogen detection in bees. However, high throughput screening for bee virus infections in singleplex PCR reactions is cumbersome and limited by the high quantities of sample RNA required. Thus, the development of a sensitive and specific multiplex PCR detection method for screening for multiple viruses simultaneously is necessary. Here, we report the development of a one-step multiplex reverse-transcription quantitative polymerase chain reaction (RT-qPCR) assay to detect four viruses commonly encountered in pollinator species. The optimized multiplex RT-qPCR protocol described in this study allows simultaneous detection of two dicistroviruses (Israeli acute paralysis virus and Black queen cell virus) and two iflaviruses (Sacbrood virus and Deformed wing virus) with high efficiency and specificity comparable to singleplex detection assays. This assay provides a broad range of detection and quantification, and the results of virus quantification in this study are similar to those performed in other studies using singleplex detection assays. This method will be particularly useful for data generation from small-bodied insect species that yield low amounts of RNA.

Developing a method to rear Varroa destructor in vitro.

Varroa destructor is a significant mite pest of western honey bees (Apis mellifera). Developing a method to rear and maintain populations of V. destructor in vitro would provide year-round access to the mites, allowing scientists to study their biology, behavior, and control more rapidly. In this study, we determined the impact of various rearing parameters on V. destructor survival and reproduction in vitro. This was done by collecting V. destructor from colonies, placing them in gelatin capsules containing honey bee larvae, and manipulating the following conditions experimentally: rearing temperature, colony source of honey bee larva, behavioral/developmental stages of V. destructor and honey bee larva, and mite:bee larva ratio. Varroa destructor survival was significantly impacted by temperature, colony source of larvae and mite behavioral stage. In addition, V. destructor reproduction was significantly impacted by mite: larva ratio, larval developmental stage, colony source of larva, and temperature. The following conditions optimized mite survival and reproduction in vitro: using a 4:1 mite:larva ratio, beginning the study with late stage uncapped larvae, using mites collected from adult bees, maintaining the rearing temperature at 34.5° C, and screening larval colony source. Ultimately, this research can be used to improve V. destructor in vitro rearing programs.

Oxalic acid application method and treatment intervals for reduction of Varroa destructor (Mesostigmata: Varroidae) populations in Apis mellifera (Hymenoptera: Apidae) colonies.

Oxalic acid (OA) is a popular miticide used to control Varroa destructor (Mesostigmata: Varroidae) in western honey bee (Apis mellifera L.) (Hymenoptera: Apidae) colonies. Our aim was to investigate which method of OA application (dribbling, fogging, or vaporizing) was the most effective at reducing V. destructor infestations (Experiment 1) and to improve upon this method by determining the treatment interval that resulted in the greatest V. destructor control (Experiment 2). We used the product Api-Bioxal (97% OA) and maintained 40 honey bee colonies (10/treatment) in both experiments. In Experiment 1, the treatments included (i) dribbling 50 ml of 3% OA solution, (ii) vaporizing 4 g of solid OA, (iii) using an insect fogger supplied with 2.5% OA dissolved in ethyl alcohol, and (iv) an untreated control. After 3 weeks, only the vaporization method reduced V. destructor infestations (from 9.24 mites/100 bees pretreatment to 3.25 mites/100 bees posttreatment) and resulted in significantly increased brood amounts and numbers of adult bees over those of the controls. In Experiment 2, all colonies were treated with 4 applications of OA via vaporization at a constant concentration of 4 g OA/colony. In this experiment, the groups were separated by treatment intervals at either 3-, 5-, or 7-day intervals. We observed that 5- and 7-day treatment intervals significantly reduced V. destructor populations from pretreatment levels over that of the controls and 3-day intervals. Our data demonstrate the efficacy of OA in reducing V. destructor infestation, particularly vaporizing 4 g every 5-7 days as the most effective method of application.

Widespread distribution of honey bee-associated pathogens in native bees and wasps: Trends in pathogen prevalence and co-occurrence.

Pollinators have experienced significant declines in the past decade, in part due to emerging infectious diseases. Historically, studies have primarily focused on pathogens in the Western honey bee, Apis mellifera. However, recent work has demonstrated that these pathogens are shared by other pollinators and can negatively affect their health. Here, we surveyed honey bees and 15 native bee and wasp species for 13 pathogens traditionally associated with honey bees. The native bee and wasp species included 11 species not previously screened for pathogens. We found at least one honey bee-associated pathogen in 53% of native bee and wasp samples. The most widely distributed and commonly detected pathogens were the microsporidian Nosema ceranae, the bacterium Melissococcus plutonius, and the viruses deformed wing virus and black queen cell virus. The prevalence of viruses was generally higher in honey bees than in native bees and wasps. However, the prevalence of M. plutonius and the brood fungus Ascosphaera apis was significantly higher in some native bee species than in honey bees. The data also reveal novel trends in the association between co-occurring pathogens in honey bees and native bees and wasps at the pathogen community level. These results can inform the assessment of risks that native pollinator species face from pathogen stress, and indicate that many non-viral pathogens, notably M. plutonius and N. ceranae, are far more widely distributed and commonly found in native bees and wasps than previously thought.

Report of amoebic disease in a colony of Western honey bees (Apis mellifera).

The amoeba Malpighamoeba mellificae is the etiologic agent of amoebic (amoeba) disease of Western honey bees (Apis mellifera). M. mellificae damages the Malpighian tubules, which is believed to weaken and kill the host bee. Here, the authors describe the detection of this organism in a honey bee colony in the Yukon Territory, Canada. The Malpighian tubules of 14% (7/50) of the adult worker bees were discolored dark brown. Fifteen bees screened using conventional polymerase chain reaction for the 18S gene of M. mellificae were positive for the pathogen. Histologically, the lumens of Malpighian tubules were packed with amoebae, causing dilation of the tubules and attenuation and loss of the tubular epithelium. This phylogenetic analysis places M. mellificae in a new clade, a sister group to the Entamoebidae. This work provides a foundation for further investigation into the distribution, prevalence, and pathology associated with M. mellificae infection.

Honey Bee (Apis mellifera) Exposure to Pesticide Residues in Nectar and Pollen in Urban and Suburban Environments from Four Regions of the United States.

The risk of honey bee (Apis mellifera L.) exposure to pesticide residues while foraging for nectar and pollen is commonly explored in the context of agroecosystems. However, pesticides are also used in urban and suburban areas for vegetation management, vector control, and the management of ornamental plants in public and private landscapes. The extent to which pesticides pose a health risk to honey bees in these settings remains unclear. We addressed this at a landscape scale by conducting pesticide residue screening analyses on 768 nectar and 862 pollen samples collected monthly over 2 years from honey bee colonies located in urban and suburban areas in eight medium to large cities in California, Florida, Michigan, and Texas (USA). A risk assessment was performed using the US Environmental Protection Agency's BeeREX model whenever an oral toxicity value was available for a compound. Chemical analyses detected 17 pesticides in nectar and 60 in pollen samples during the survey. Approximately 73% of all samples contained no detectable pesticide residues. Although the number of detections varied among the sampled regions, fewer pesticides were detected in nectar than in pollen. Per BeeREX, four insecticides showed a potential acute risk to honey bees: imidacloprid, chlorpyrifos, and esfenvalerate in nectar, and deltamethrin in nectar and pollen. In general, exposure of honey bees to pesticides via nectar and pollen collection was low in urban and suburban areas across the United States, and no seasonal or spatial trends were evident. Our data suggest that honey bees are exposed to fewer pesticides in developed areas than in agricultural ones. Environ Toxicol Chem 2022;41:991-1003. © 2022 SETAC.

Testing new compounds for efficacy against Varroa destructor and safety to honey bees (Apis mellifera).

BACKGROUND: Varroa destructor is among the greatest threats to honey bee health worldwide. Acaricides used to control Varroa are becoming increasingly ineffective due to resistance issues, prompting the need for new compounds that can be used for control purposes. Ideally, such compounds would exhibit high toxicity to Varroa while maintaining relatively low toxicity to bees and beekeepers. We characterized the lethal concentrations (LC50 ) of amitraz, matrine, FlyNap®, the experimental carbamates 2-((2-ethylbutyl)thio)phenyl methylcarbamate (1) and 2-(2-ethylbutoxy)phenyl methylcarbamate (2), and dimethoate (positive control) for Varroa using a glass vial assay. The test compounds also were applied to honey bees using an acute contact toxicity assay to determine the adult bee LD50 for each compound. RESULTS: Amitraz was the most toxic compound to Varroa, but carbamate 2 was nearly as active (within 2-fold) and the most selective due to its lower bee toxicity, demonstrating its promise as a Varroa control. While carbamate 1 was less toxic to honey bees than was amitraz, it was also 4.7-fold less toxic to the mites. Both matrine and FlyNap® were relatively ineffective at killing Varroa and were moderately toxic to honey bees. CONCLUSION: Additional testing is required to determine if carbamate 2 can be used as an effective Varroa control. As new chemical treatments are identified, it will be necessary to determine how they can be utilized best alongside other control techniques as part of an integrated pest management program. © 2021 Society of Chemical Industry.

CropPol: A dynamic, open and global database on crop pollination.

Seventy five percent of the world's food crops benefit from insect pollination. Hence, there has been increased interest in how global change drivers impact this critical ecosystem service. Because standardized data on crop pollination are rarely available, we are limited in our capacity to understand the variation in pollination benefits to crop yield, as well as to anticipate changes in this service, develop predictions, and inform management actions. Here, we present CropPol, a dynamic, open, and global database on crop pollination. It contains measurements recorded from 202 crop studies, covering 3,394 field observations, 2,552 yield measurements (i.e., berry mass, number of fruits, and fruit density [kg/ha], among others), and 47,752 insect records from 48 commercial crops distributed around the globe. CropPol comprises 32 of the 87 leading global crops and commodities that are pollinator dependent. Malus domestica is the most represented crop (32 studies), followed by Brassica napus (22 studies), Vaccinium corymbosum (13 studies), and Citrullus lanatus (12 studies). The most abundant pollinator guilds recorded are honey bees (34.22% counts), bumblebees (19.19%), flies other than Syrphidae and Bombyliidae (13.18%), other wild bees (13.13%), beetles (10.97%), Syrphidae (4.87%), and Bombyliidae (0.05%). Locations comprise 34 countries distributed among Europe (76 studies), North America (60), Latin America and the Caribbean (29), Asia (20), Oceania (10), and Africa (7). Sampling spans three decades and is concentrated on 2001-2005 (21 studies), 2006-2010 (40), 2011-2015 (88), and 2016-2020 (50). This is the most comprehensive open global data set on measurements of crop flower visitors, crop pollinators and pollination to date, and we encourage researchers to add more datasets to this database in the future. This data set is released for non-commercial use only. Credits should be given to this paper (i.e., proper citation), and the products generated with this database should be shared under the same license terms (CC BY-NC-SA).

Attack of the dark clones the genetics of reproductive and color traits of South African honey bees (Apis mellifera spp.).

The traits of two subspecies of western honey bees, Apis mellifera scutellata and A.m. capensis, endemic to the Republic of South Africa (RSA), are of biological and commercial relevance. Nevertheless, the genetic basis of important phenotypes found in these subspecies remains poorly understood. We performed a genome wide association study on three traits of biological relevance in 234 A.m. capensis, 73 A.m. scutellata and 158 hybrid individuals. Thirteen markers were significantly associated to at least one trait (P ≤ 4.28 × 10-6): one for ovariole number, four for scutellar plate and eight for tergite color. We discovered two possible causative variants associated to the respective phenotypes: a deletion in GB46429 or Ebony (NC_007070.3:g.14101325G>del) (R69Efs*85) and a nonsense on GB54634 (NC_007076.3:g.4492792A>G;p.Tyr128*) causing a premature stop, substantially shortening the predicted protein. The mutant genotypes are significantly associated to phenotypes in A.m. capensis. Loss-of-function of Ebony can cause accumulation of circulating dopamine, and increased dopamine levels correlate to ovary development in queenless workers and pheromone production. Allelic association (P = 1.824 x 10-5) of NC_007076.3:g.4492792A>G;p.Tyr128* to ovariole number warrants further investigation into function and expression of the GB54634 gene. Our results highlight genetic components of relevant production/conservation behavioral phenotypes in honey bees.

Mitigating Nosema ceranae infection in western honey bee (Apis mellifera) workers using propolis collected from honey bee and stingless bee (Tetrigona apicalis) hives.

Beekeepers need sustainable control options to treat Nosema ceranae infection in colonies of western honey bees (Apis mellifera L.) they manage. Propolis is a natural product derived from plant resins and contains chemical compounds with potential antimicrobial activity against N. ceranae. Here, we determined the efficacy of propolis from A. mellifera (USA) and Tetrigona apicalis (stingless bees, Thailand) colonies as treatments for N. ceranae infection in honey bee workers. Newly emerged bees were individually fed 2 µL of 50% (w/v) sucrose solution containing 1 × 105N. ceranae spores. Following this, the infected bees were treated with 50% propolis extracted from A. mellifera or T. apicalis hives and fed in 50% sucrose solution (v/v). All bees were maintained at 34 ± 2 °C and 55 ± 5% RH. Dead bees were counted daily for 30 d to calculate survival. We also determined infection rate (# infected bees/100 bees), infectivity (number of spores per bee) and protein content in the hypopharyngeal glands and hemolymph on 7, 14, and 21 d post infection as measures of bee health. Propolis from both bee species significantly reduced bee mortality, infection rate and infectivity compared with those of untreated bees and led to significantly greater protein contents in hypopharyngeal glands and hemolymph in treated bees than in untreated ones (p < 0.0001). In conclusion, propolis from A. mellifera and T. apicalis colonies shows promise as a control against N. ceranae infection in honey bees.

Integrated Pest Management Control of Varroa destructor (Acari: Varroidae), the Most Damaging Pest of (Apis mellifera L. (Hymenoptera: Apidae)) Colonies.

Varroa destructor is among the greatest biological threats to western honey bee (Apis mellifera L.) health worldwide. Beekeepers routinely use chemical treatments to control this parasite, though overuse and mismanagement of these treatments have led to widespread resistance in Varroa populations. Integrated Pest Management (IPM) is an ecologically based, sustainable approach to pest management that relies on a combination of control tactics that minimize environmental impacts. Herein, we provide an in-depth review of the components of IPM in a Varroa control context. These include determining economic thresholds for the mite, identification of and monitoring for Varroa, prevention strategies, and risk conscious treatments. Furthermore, we provide a detailed review of cultural, mechanical, biological, and chemical control strategies, both longstanding and emerging, used against Varroa globally. For each control type, we describe all available treatments, their efficacies against Varroa as described in the primary scientific literature, and the obstacles to their adoption. Unfortunately, reliable IPM protocols do not exist for Varroa due to the complex biology of the mite and strong reliance on chemical control by beekeepers. To encourage beekeeper adoption, a successful IPM approach to Varroa control in managed colonies must be an improvement over conventional control methods and include cost-effective treatments that can be employed readily by beekeepers. It is our intention to provide the most thorough review of Varroa control options available, ultimately framing our discussion within the context of IPM. We hope this article is a call-to-arms against the most damaging pest managed honey bee colonies face worldwide.

Tracing the Fate of Pollen Substitute Patties in Western Honey Bee (Hymenoptera: Apidae) Colonies.

Commercial beekeepers need healthy, productive honey bee (Apis mellifera L.) colonies, even when the landscape lacks adequate pollen forage to sustain the colonies. As a result, many commercial beekeepers spend significant money and labor on the use of pollen substitutes in their colonies. However, there is little consensus in the literature about the benefits and drawbacks of pollen substitute use on honey bee colony health. In order to understand this critically, it is important to know first how honey bees distribute pollen substitute patties throughout their colonies. We traced the fate of three commercially available pollen substitute patties (MegaBee, UltraBee, AP23) dyed with a nontoxic food coloring (Brilliant Blue FCF) and undyed as negative controls, a dyed positive control (fondant), and a dyed consumption control (Crayola Model Magic Clay) in 44 honey bee colonies. Using spectrophotometry and visual inspection, we analyzed adult bee guts, larval guts, bee bread stores and colony debris underneath the hive for presence of the dye. Our data suggest that (1) a proportion of adult bees ingest the patty, (2) adult bees likely do not feed patty directly to larvae, (3) adult bees do not store patty like bee bread, and (4) only a very small proportion of patty is lost as debris. Collectively our data suggest that honey bee colonies use pollen substitute patties. However, patties likely do not replace the function of natural pollen entirely in terms of larval provisioning and long-term storage as bee bread.

Detection of Lotmaria passim, Crithidia mellificae and Replicative Forms of Deformed Wing Virus and Kashmir Bee Virus in the Small Hive Beetle (Aethina tumida).

Knowledge regarding the honey bee pathogens borne by invasive bee pests remains scarce. This investigation aimed to assess the presence in Aethina tumida (small hive beetle, SHB) adults of honey bee pathogens belonging to the following groups: (i) bacteria (Paenibacillus larvae and Melissococcus plutonius), (ii) trypanosomatids (Lotmaria passim and Crithidia mellificae), and (iii) viruses (black queen cell virus, Kashmir bee virus, deformed wing virus, slow paralysis virus, sacbrood virus, Israeli acute paralysis virus, acute bee paralysis virus, chronic bee paralysis virus). Specimens were collected from free-flying colonies in Gainesville (Florida, USA) in summer 2017. The results of the molecular analysis show the presence of L. passim, C. mellificae, and replicative forms of deformed wing virus (DWV) and Kashmir bee virus (KBV). Replicative forms of KBV have not previously been reported. These results support the hypothesis of pathogen spillover between managed honey bees and the SHB, and these dynamics require further investigation.

The Larvicidal and Adulticidal Effects of Selected Plant Essential Oil Constituents on Greater Wax Moths.

Some plant essential oil constituents, such as monoterpenoids and phenylpropanoids, are promising insecticides in some situations and for certain insect pests. They vary in their toxicity, depending on the target insect. Moths (Lepidoptera) appear susceptible to these compounds, making them of promise for use against greater wax moths (Galleria mellonella Fabricius, (Lepidoptera: Pyrallidae), GWM), an important pest of western honey bee (Apis mellifera Linnaeus. (Hymenoptera: Apidae)) colonies. We determined the LC50 for GWM larvae or LD50 for GWM adults of select compounds (thymol, carvacrol, (S)-(+)-carvone, estragole, citral, linalool, (S)-(-)-limonene, and γ-terpinene). Concentrations between 8 and 2,266 µg/cm3 were mixed into the diets of GWM larvae and doses ranging between 0.08 and 70.3 mg per adult were applied topically to the abdomens of GWM adults. Lethal concentrations and doses were calculated after of 72 h of exposure. All eight compounds showed insecticidal activity against all tested stages of GWMs. Thymol (LC50 µg/cm3 (95% CI) = 21 [9-56], carvacrol = 46 [26-79], citral = 63 [30-134], and carvone = 76 [33-201]) had the highest toxicity toward GWM larvae. The hydrocarbons limonene (296 [231-377]), estragole (466 [354-611]), and γ-terpinene (729 [630-857]) had the lowest toxicity toward GWM larvae. Thymol had the highest toxicity towards GWM adults (LD50 (CI) = 0.5 [0.4-0.8] mg/adult). However, carvacrol (11.6 [10.1-13.6]), linalool (12.9 [9.3-17.8]), and limonene (15.8 [13.1-19.2]) were less toxic to GWM larvae. Our data show that select plant essential oil constituents are promising controls of GWM.

The complete mitochondrial genome of Apis mellifera jemenitica (Insecta: Hymenoptera: Apidae), the Arabian honey bee.

The mitochondrial genome of a worker Apis mellifera jemenitica was 16,623 bp. It consisted of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and a control region. Phylogenetic analyses suggest a close relationship between A. m. jemenitica, A. m. lamarckii and A. m. syriaca.

The mitochondrial genome of the Maltese honey bee, Apis mellifera ruttneri (Insecta: Hymenoptera: Apidae).

The mitochondrial genome of Apis mellifera ruttneri consisted of 13 protein-coding genes, two rRNAs, 22 tRNAs, an AT-rich control region, and was 16,577 bp long. The phylogenetic analyses suggested that A. m. ruttneri was closely related to two North African subspecies: A. m. sahariensis and A. m. intermissa.

Successful Pupation of Small Hive Beetle, Aethina tumida (Coleoptera: Nitidulidae), in Greenhouse Substrates.

The small hive beetle, Aethina tumida Murray, is an invasive pest that has spread globally. Western honey bees, Apis mellifera Linnaeus (Hymenoptera: Apidae), are considered the most important host and infestations can lead to collapse of colonies. Larvae feed on honey, pollen, and brood inside the hive and leave the hive as postfeeding wandering larvae to pupate in the surrounding soil. Other host species include bumble bees, stingless bees, and solitary bees, all of which can facilitate small hive beetle reproduction and are used for greenhouse crop pollination worldwide. Here, we investigated if small hive beetles can complete their life cycle when soil is absent by pupating in plant root-supporting substrates commonly used in greenhouses. Wandering small hive beetle larvae were introduced into containers with coconut fiber, perlite, a mixture of both and stone wool substrates to investigate pupation success and development time. Sand was used as control substrate. In all but one substrate (perlite), small hive beetles developed into adults equally well as they did in the sand. Development time ranged between 23 and 37 d and was not different from that of the control. We showed that small hive beetles can pupate in greenhouse substrates. This could constitute a problem for greenhouse pollination as well as it could facilitate small hive beetle survival in areas which otherwise would be deemed unsuitable or marginal environments for small hive beetles to become established. Our study highlights the opportunistic nature of the small hive beetle as an invasive species.

Comparing four methods of rearing Varroa destructor in vitro.

The parasitic mite Varroa destructor Anderson and Trueman continues to devastate western honey bee (Apis mellifera L.) colonies throughout most of the world where they are managed. The development of a method to rear Varroa in vitro would allow for year-round Varroa research, rapidly advancing our progress towards controlling the mite. We created two separate experiments to address this objective. First, we determined which of four in vitro rearing methods yields the greatest number of Varroa offspring. Second, we attempted to improve the rearing rates achieved with that method. The four methods tested included (1) rearing Varroa on honey bee pupae in gelatin capsules, (2) rearing Varroa on in vitro-reared honey bees, (3) group rearing Varroa on honey bee pupae in Petri dishes, and (4) providing Varroa a bee-derived diet. The number of reproducing females and the number of fully mature offspring were significantly higher in the gelatin capsules maintained at 75% RH than in any other method. A 2 × 3 full factorial design was used to test combinations of gelatin capsule size (6 and 7 mm diameter) and relative humidity (65, 75, or 85%) on Varroa rearing success. Varroa reproduction and survival were significantly higher in 7-mm-diameter gelatin capsules maintained at 75% RH than in those maintained in 6-mm capsules and at the other humidities. By identifying factors that influence Varroa reproductive success in vitro, this work provides an important foundation for the development of future rearing protocols.

Evaluating the Efficacy of Oxalic Acid Vaporization and Brood Interruption in Controlling the Honey Bee Pest Varroa destructor (Acari: Varroidae).

A successful Integrated Pest Management approach to Varroa destructor Anderson and Trueman control in managed colonies of western honey bees Apis mellifera Linnaeus (Hymenoptera: Apidae) must be an improvement over conventional control methods and include cost-effective treatments that can be readily employed by beekeepers. Herein, we tested the efficacy of oxalic acid (OA) vaporization and brood interruption as Varroa controls. Sixty experimental colonies were randomly assigned to one of six treatment groups with 10 colonies per group. The six treatments were: 1) OA applied once, 2) OA applied three times, 3) brood interruption, 4) OA applied once + brood interruption, 5) OA applied three times + brood interruption, and 6) no OA or brood interruption. The OA was applied via vaporization, with each application being 1 g OA applied through the hive entrance (label rate), on the bottom board. Brood interruption was accomplished by caging a colony's queen in a queen cage for a period of 24 d. An additional 10 colonies were treated with amitraz (Apivar - positive control). Varroa levels were estimated before, during, and after treatment applications using sticky boards left in colonies for 3 d. Our data suggest that queen caging to achieve brood interruption during the fall season can negatively impact colony strength and survival. We observed high colony mortality in some treatments, despite diligent colony management to alleviate the side effects of the treatments. Colonies treated with amitraz were healthier and had better survival than those treated with OA vaporization. In conclusion, OA and/or brood interruption did not provide sufficient Varroa control.

Genetic diversity and population structure of two subspecies of western honey bees (Apis mellifera L.) in the Republic of South Africa as revealed by microsatellite genotyping.

Apis mellifera scutellata and Apis mellifera capensis, two native subspecies of western honey bees in the Republic of South Africa (RSA), are important to beekeepers in their native region because beekeepers use these bees for honey production and pollination purposes. Additionally, both bees are important invasive pests outside of their native ranges. Recently, whole mitogenome sequencing and single nucleotide polymorphisms were used to study their genetic diversity. To add to our knowledge of the molecular ecology of both bees, we tested the ability of microsatellites to be used as a tool to discriminate between A.m. capensis and A.m. scutellata. We analyzed the genetic variability and overall population structure of both bee subspecies and hybrids of the two by genotyping individuals collected from RSA (N = 813 bees from 75 apiaries) at 19 microsatellite DNA loci. Overall, populations averaged between 9.2 and 11.3 alleles per locus, with unbiased heterozygosity values ranging from 0.81 to 0.86 per population. Bayesian clustering analyses revealed two distinct evolutionary units, though the results did not match those of earlier morphometric and molecular analyses. This suggests that the microsatellites we tested were not sufficient for subspecies identification purposes, especially for Cape and hybrid bees. Nevertheless, the microsatellite data highlight the considerable genetic diversity within both populations and a larger-than-expected hybridization zone between the natural distributions of A.m. capensis and A.m. scutellata.