It is difficult to assess the relative influence of anthropogenic processes (e.g., habitat fragmentation) versus species’ biology on the level of genetic differentiation among populations when species are restricted in their distribution to fragmented habitats. This issue is particularly problematic for Australian rock-wallabies (Petrogale sp.), where most previous studies have examined threatened species in anthropogenically fragmented habitats. The short-eared rock-wallaby (Petrogale brachyotis) provides an opportunity to assess natural population structure and gene flow in relatively continuous habitat across north-western Australia. This region has reported widespread declines in small-to-medium sized mammals, making data regarding the influence of habitat connectivity on genetic diversity important for broad-scale management. Using non-invasive and standard methods, 12 microsatellite loci and mitochondrial DNA were compared to examine patterns of population structure and dispersal among populations of P. brachyotis in the Kimberley, Western Australia. Low genetic differentiation was detected between populations separated by up to 67 km. The inferred genetic connectivity of these populations suggests that in suitable habitat P. brachyotis can potentially disperse far greater distances than previously reported for rock-wallabies in more fragmented habitat. Like other Petrogale species male-biased dispersal was detected. These findings suggest that a complete understanding of population biology may not be achieved solely by the study of fragmented populations in disturbed environments and that management strategies may need to draw on studies of populations (or related species) in undisturbed areas of contiguous habitat.