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.