Freshwater crayfish are a highly diverse group of decapod crustaceans that are distributed across all but the Indian and Antarctic continents. Their broad distribution suggests a strong ability to disperse and adapt to a wide range of habitats and environmental niches. In particular, freshwater crayfish have been discovered in caves, burrows, streams, lakes and sometimes even terrestrial habitats. This dispersed distribution across a range of habitats is particularly evident for the genus Cherax, with at least 47 species identified from throughout Australia. With some species highly diverse and others widely distributed, it is unclear what effect geographic, behavioural and ecological isolation has had on the current biogeographic structure of Australian Cherax. By investigating variation across a nested series of scales, the primary aim of this study was to distinguish the historical and contemporary drivers that may have caused and maintained the high level of biodiversity observed in Australian and more specifically South-East Queensland (SEQ) Cherax.