Due to anthropogenic and natural impacts (environmental changes and disease outbreaks) many formerly widespread bovid species now exist only as managed populations on private land and in isolated formally protected areas, especially in South Africa. Natural ecological processes, such as migration (and consequent gene flow), and evolutionary processes, such as local adaptation and reinforcement of differentiation, currently occur on a limited scale. Instead managers need to mimic natural migration through translocations and the re-establishment of dispersal corridors between isolated areas. Due to changes in the distribution patterns of populations, subspecies and species, local adaptation is broken down due to outcrossing and outbreeding, or due to other changes in selection regimes. Varied management strategies across different conservation areas and on private lands further exacerbate the situation. We are using studies of genetic variation, based on markers that provide resolution across different time scales, to infer the evolutionary and ecological processes that have operated across populations of large and small antelope species. These insights can be used by managers to identify the most feasible options for maintaining the short- and long-term benefits of these processes that ultimately contribute to species persistence. Our research also questions previous subspecies and species descriptions and what we know about distribution records.