Black and white rhinoceros (Diceros bicornis and Ceratotherium simum) are iconic African species that are classified by the International Union for the Conservation of Nature (IUCN) as Critically Endangered and Near Threatened (http://www.iucnredlist.org/), respectively [1]. At the end of the 19 century, Southern white rhinoceros (Ceratotherium simum simum) numbers had declined to fewer than 50 animals in the Hluhluwe-iMfolozi region of the KwaZulu-Natal (KZN) province of South Africa, mainly due to uncontrolled hunting [2,3]. Efforts by the Natal Parks Board facilitated an increase in population to over 20,000 in 2015 through aggressive conservation management [2]. Black rhinoceros (Diceros bicornis) populations declined from several hundred thousand in the early 19 century to ∼65,000 in 1970 and to ∼2,400 by 1995 [1] with subsequent genetic reduction, also due to hunting, land clearances and later poaching [4]. In South Africa, rhinoceros poaching incidents have increased from 13 in 2007 to 1,215 in 2014 [1]. This has occurred despite strict trade bans on rhinoceros products and strict enforcement in recent years.

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Wildlife is a multi-million dollar industry in South Africa ranging from intensively farmed animals on small properties to free-roaming animals in large functional ecosystems. Specific concerns surrounding the conservation value of the intensively managed wildlife have been raised. Increasingly it is recognised that genetics must be considered when developing conservation policy and management practices. Minimal genetic data are available to assist with decisions within the industry.Microsatellite markers have been developed for some species and are currently used for individual identification, parentage assessment and to inform translocation decisions. However, validation for standardized application in wildlife management has not been completed. Common species for which conservation management decisions have to be made include: Cape buffalo (Syncerus caffer), blue wildebeest (Connochaetes taurinus taurinus), common impala (Aepyceros melampus) and sable antelope (Hippotragus niger). Using existing microsatellite markers for domestic and wild species, we have developed multiplex panels for use in these species. We discriminated between 751 buffalo (four pairs were not distinguishable), 1307 blue wildebeest (three pairs were not distinguishable), 580 impala and 493 sable antelope. We determined parentage in four case studies using a combination of microsatellite and demographic data. We also tested microsatellite markers on roan antelope (Hippotragus equinus), gemsbok (Oryx gazella) and eland (Tragelaphus oryx) and report preliminary data. Further research to improve this validation includes: extensive sampling from more diverse areas, targeted or full genome sequencing to identify additional microsatellite loci, development of sampling kits and training of veterinarians, as well as expansion of the species tested.