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Abstract Hybridization in antelope species has been widely reported in South African national parks and provincial reserves as well as on private land due to anthropogenic effects. In a closed management setting, hybridization may occur due to the crossbreeding of closely related species with unequal sex ratios, resulting in either sterile or fertile offspring. In this study, we used molecular techniques to evaluate the risk of anthropogenic hybridization between blesbok (Damaliscus pygargus phillipsi) and red hartebeest (Alcelaphus buselaphus caama) in an isolated group that purposely included the two species with unequal sex ratios (one red hartebeest male and 19 male and female blesbok). Genetic analysis based on microsatellites confirmed the presence of seven hybrid individuals. Mitochondrial analysis verified that hybridization occurred between blesbok females and the red hartebeest male. STRUCTURE and NEWHYBRIDS classified the hybrids as F1. It is suspected that the hybrid individuals were sterile as the males had undeveloped testes and only F1 hybrids were detected. Thus, the risk of hybridization between these two species may be limited in the wild. In captive settings, genetic monitoring should be included in management plans for blesbok and red hartebeest to ensure that the long‐term consequences of wasted reproductive effort are limited.

Abstract Anthropogenic hybridization is an increasing conservation threat worldwide. In South Africa, recent hybridization is threatening numerous ungulate taxa. For example, the genetic integrity of the near‐threatened bontebok (Damaliscus pygargus pygargus) is threatened by hybridization with the more common blesbok (D. p. phillipsi). Identifying nonadmixed parental and admixed individuals is challenging based on the morphological traits alone; however, molecular analyses may allow for accurate detection. Once hybrids are identified, population simulation software may assist in determining the optimal conservation management strategy, although quantitative evaluation of hybrid management is rarely performed. In this study, our objectives were to describe species‐wide and localized rates of hybridization in nearly 3,000 individuals based on 12 microsatellite loci, quantify the accuracy of hybrid assignment software (STRUCTURE and NEWHYBRIDS), and determine an optimal threshold of bontebok ancestry for management purposes. According to multiple methods, we identified 2,051 bontebok, 657 hybrids, and 29 blesbok. More than two‐thirds of locations contained at least some hybrid individuals, with populations varying in the degree of introgression. HYBRIDLAB was used to simulate four generations of coexistence between bontebok and blesbok, and to optimize a threshold of ancestry, where most hybrids will be detected and removed, and the fewest nonadmixed bontebok individuals misclassified as hybrids. Overall, a threshold Q‐value (admixture coefficient) of 0.90 would remove 94% of hybrid animals, while a threshold of 0.95 would remove 98% of hybrid animals but also 8% of nonadmixed bontebok. To this end, a threshold of 0.90 was identified as optimal and has since been implemented in formal policy by a provincial nature conservation agency. Due to widespread hybridization, effective conservation plans should be established and enforced to conserve native populations that are genetically unique.