Within the southwestern Australian biodiversity hotspot, the Shark Bay region displays high levels of plant and animal endemism, particularly in the herpetofauna. The region has been subjected to dramatic climatic fluctuations and has been geologically active from the Late Miocene to the present. The myobatrachid frog Arenophryne rotunda, a Shark Bay endemic, provides an ideal opportunity to examine the relative effects of fluctuating climates and geological activity on the biota of Shark Bay. A comprehensive phylogeographic analysis of A. rotunda, based on data comprising 1154 bp of the mitochondrial gene ND2, is presented. My results demonstrate a major genetic break that divides this species at the northern edge of the Victorian Plateau into northern and southern species lineages, dating to the Late Miocene, with a further division of the southern species lineage across the Murchison Gorge dating to the Plio-Pleistocene border. Both of these periods are related to prominent geological activity and climatic shifts in the Shark Bay region. Interpretation of phylogeographic results point to the prominent role of fluctuating Pleistocene climates and associated coastal landscape evolution in the generation of phylogeographic structure within the distinct A. rotunda species lineages. Similar processes have been invoked to explain the diversity of other Shark Bay biota.