Genetic diversity is a critical determinant of the persistence of populations because it enables animals to evolve and adapt to environmental change. Black-footed rock-wallabies (Petrogale lateralis MacDonnell Ranges race), or warru, once occupied virtually all suitable habitat within the arid zone of central Australia. However, only two metapopulations now remain in the southern portion of this race’s range (South Australia) and a recovery program has involved both in- and ex-situ conservation initiatives. To establish whether genetic factors such as inbreeding may be inhibiting population recovery, the current study examined the population structure and genetic diversity of animals in the three largest-known extant colonies using six polymorphic microsatellite loci. Bayesian and frequency-based assignment tests revealed substantial population structuring (pairwise F_ST values 0.122–0.278), congruent with geographically distinct colonies. There was some evidence of dispersal, with two migrants identified across two colonies, but little evidence for extensive interbreeding among colonies. Population substructure was evidenced by high values of F_IS in one colony. All populations possessed relatively high levels of genetic diversity (allelic richness: 5.1–7.5, heterozygosity: 0.70–0.72). On the basis of a genetic analysis of parentage, approximately half of all males and females in the known metapopulations produced offspring. This has likely contributed to the retention of genetic diversity across colonies. These findings have implications for the management of both the in- and ex-situ warru populations.