Dispersal plays an important role in the population structure and resilience of species. To gain a better understanding of dispersal in the endangered Australian marsupial, the dibbler (Parantechinus apicalis), we screened 199 individuals from seven locations within the Fitzgerald River National Park, Western Australia, for genetic variation at 17 microsatellite loci. There were high levels of genetic variation within all sites (gene diversity ranged from 0.68 to 0.71) as well as significant genetic differentiation between sites less than 19 km apart that were consistent over multiple years (FST = 0.021–0.073). A Bayesian clustering analysis revealed the presence of two genetic clusters separating P. apicalis in the western part from the central and eastern parts of the National Park. There was also evidence of fine-scale population structure with spatial autocorrelation analysis showing positive genetic structure up to distances of 200 m in females. By contrast males did not exhibit significant fine-scale population structure, thus suggesting P. apicalis exhibits female philopatry and male-biased dispersal. We recommend that management should take into account the existence of two subpopulations within the National Park and manage accordingly. Individuals selected for captive breeding and translocation programs, especially females, should be sampled at least 200 m apart to reduce the likelihood of selecting related individuals.