The irregular nature of rainfall in the Australian arid and semiarid zones results in a heterogeneous distribution of resources in both time and space. The mammal species that reside in these regions are uniquely adapted to these climatic conditions, often occurring in naturally low densities and increasing significantly in numbers following major rainfall events. We investigated how these adaptations may influence genetic diversity and gene flow across the landscape in an endangered semiarid/arid-zone marsupial, the sandhill dunnart (Sminthopsis psammophila), from three known populations in southern Australia. Analyses of mitochondrial control region (CR) sequences and microsatellite loci revealed that S. psammophila had maintained similar levels of genetic diversity to other sympatric Sminthopsis species despite its endangered status. There was no evidence for significant phylogeographic structure within the species, but each population was genetically differentiated, based on the frequency of microsatellite alleles and CR haplotypes, suggesting that they should be considered as distinct Management Units for conservation. At a fine spatial scale, no significant genetic structure or sex-biased dispersal was detected within a study site of 240 km². These findings suggest that both sexes are highly mobile, which allows individuals to locate localised resource patches when they become available. We detected evidence of a genetic bottleneck within the population, possibly caused by a recent drought. Our study highlights the importance of maintaining connectivity across the landscape for semiarid- and arid-zone species to enable them to track resource pulses and maintain genetic diversity.