Aim: The complexity and biologically challenging nature of arid landscapes can generate high inter- and intra-species diversity, although these biomes remain poorly studied. We investigated whether prominent geomorphic features in an Australian arid landscape had similar influences on patterns of intra-specific genetic diversity of three small mammals with different distribution and life history traits. Specifically, we tested (1) whether mountain ranges harbour high diversity and act as refugia, (2) the extent to which ephemeral river systems pose barriers to gene flow, or (3) whether environmental differences explain genetic structure in these species. Location: The topographically complex Pilbara bioregion of the Australian arid zone. Taxa: Two native rodents, the Western pebble-mound mouse, Pseudomys chapmani, and the Sandy inland mouse, Pseudomys hermannsburgensis, and a dasyurid, Ningaui timealeyi. Methods: We used maximum parsimony networks of mitochondrial haplotypes and spatially-explicit Bayesian clustering analysis of microsatellite genotypes to identify historical and contemporary genetic structure in each species. Based on measures of individual diversity and genetic distance, we distinguished ‘hotspots’ and ‘coldspots’ (greater than 1.5 standard deviations from the mean) of genetic diversity and genetic connectivity and assessed their concordance with landscape features. The influence of environmental dissimilarity on observed genetic differentiation was evaluated using generalised dissimilarity modelling. Results: Patterns of genetic diversity and connectivity were complex, with few consistent patterns across species. Both microsatellite and mitochondrial diversity were high across species, with limited spatial genetic structure. Rivers had the most influence on genetic patterns but were not consistently identified as barriers. Environmental dissimilarity amongst sampling sites had low explanatory power. Main Conclusions: Limited genetic structure in each of the three species suggests that the structurally complex Pilbara landscape remains relatively permeable to species with high dispersal capacity. Additionally, population responses to boom-bust cycles in arid environments are likely to obscure spatial genetic patterns.