Habitat destruction is one of the leading threats to biodiversity. It results in the contraction and fragmentation of species’ distributions, enhancing the potential for extinction through the isolation of species in small populations. For conservation of threatened species, it is important to assess how fragmentation influences genetic connectivity of populations. The latter is dependent on the biology of individual species and the nature of the intervening matrix. In this study, we investigated genetic connectivity for an endangered marsupial, the southern brown bandicoot (Isoodon obesulus obesulus) from a fragmented forest system in south-east South Australia. We genotyped 15 microsatellite loci from 147 samples collected from 14 native forest patches, each surrounded by a matrix of either Pinus radiata plantation or cleared agricultural land. Our results showed significant population genetic structuring at a fine spatial scale in the 520 km2 Mount Burr region, with samples grouping into three population clusters. Evidence for dispersal among habitat patches was limited and dispersal generally only occurred among neighbouring patches. Overall, the genetic structuring we have observed is likely to have resulted from fragmentation of the landscape. Our findings contribute crucial information for the physical positioning of habitat corridors in this area, and provide baseline data to enable the effectiveness of these corridors to be assessed in the future.