To assess phylogeographic pattern throughout the range of Metacrinia nichollsi in order to develop specific biogeographical hypotheses for the wet forests of south-western Australia. This was carried out by contrasting a direct-developing frog species, M. nichollsi, that breeds independently of free surface water with conventional, aquatic breeders and highly specialized direct developers. Wet forests of the south-western Australian biodiversity hotspot - an area of high species richness and endemism for myobatrachid frogs and many other faunal groups. We compiled an extensive phylogeographic data set from field-collected samples based on mitochondrial ND2 sequences. Phylogenetic analyses combined with estimates of divergence times were used to build a model of major biogeographical events affecting the species. Phylogeographic analyses were used to provide insights into smaller-scale processes acting within each major lineage. Phylogenetic analysis recovered three major lineages, with divergence dates coincident with late Miocene-early Pliocene arid cycles. One lineage was confined to geographically isolated populations in the Stirling Ranges (Stirling Ranges Lineage, SRL). The continuous range of M. nichollsi was split into two: the Main Range Lineage (MRL) and the Southern Coastal Lineage (SCL). The SCL displays a strong drainage-based population structure, whereas the MRL displays a strong signature of recent expansion, suggesting that these two lineages have had very different biogeographical histories. Late Miocene-Pliocene aridity appears to have isolated populations in the Stirling Ranges and resulted in the formation of two additional lineages on a north-south gradient that are independent of southward-flowing drainage systems. Our results demonstrate that climatic fluctuations are likely to have generated fine-scale phylogeographic structure within M. nichollsi and that catchment regions are important refugia during arid cycles.