Islands provide the last refuge for many Australian species that have succumbed to range contractions since European settlement. These species have heightened vulnerability when developments are planned for the islands. The burrowing bettong (Bettongia lesueur), a threatened macropod, was once widespread across Australia but now occurs naturally only on Barrow Island and two other Western Australian offshore islands. Here, we document the demographic, social and genetic characteristics of the Barrow Island population, using nuclear microsatellites, mtDNA and demographic parameters from 286 individuals trapped around 29 warrens. The Barrow Island population utilises complex warren systems scattered across the landscape and exhibits continuous breeding, even during extensive dry conditions. Males (759 g) were significantly heavier than females (735 g), with the latter reaching sexual maturity at ∼600 g. Warrens varied markedly in size and number of individuals, with 20% of females and 25% of males moving between nearby warrens. There were two deep mtDNA haplotype clades that coalesce around 298 000 years ago, indicating that this island population has maintained an effective population size that has permitted the retention of one marked feature of its preisolation genetic diversity. Dispersal and gene flow between warrens was severely constrained. Both mtDNA and 11 nuclear microsatellites showed a strong isolation by distance effect, with genetic differences between warrens increasing linearly with geographic separation. While this was marked in both sexes, it was stronger in females and consistent with shorter dispersal distances for females than for males. The trapping and genetic data are concordant, with between-warren sociality correlated with genetic similarity. Long-term conservation, management and translocation programs will benefit from cognisance of the strong fidelity to natal areas, as evidenced by both recapture data and genetic analyses.