Information on genetic variation within and among populations is relevant for a broad range of topics in biology. We use a combination of mitochondrial and nuclear microsatellite markers to evaluate genetic variation within and between two populations of bat-eared foxes (Otocyon megalotis Desmarest, 1822) in South Africa. The bat-eared fox is a small canid occurring in southern and eastern Africa. The species is currently not threatened with extinction, but a lack of information on genetic diversity has been identified as a deficit for its future conservation. We observed low to moderate genetic differentiation between the two geographically separated populations, but neither mitochondrial nor nuclear microsatellite markers suggested that there have been dispersal barriers between them. Similar genetic diversity within both populations was contrasted by interpopulational differences in relatedness variation among males and females. A high genetic relatedness within both populations, indicated by mitochondrial data, is likely caused by a common historical origin or a combination of species-specific social organization and environmental dispersal constraints. We call for further research on the genetic divergence of bat-eared fox populations as well as on the genetic consequences of interactions between environmental characteristics and social organization in this species.