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Recent molecular and morphological analyses have shown that chiltoniid amphipods, once thought to be a relictual group, are a diverse and speciose family of Australian freshwater amphipods. As part of a larger examination of the family, chiltoniids from Kangaroo Island in South Australia were collected and analysed using molecular (COI and 28S) and morphological methods in order to understand species distributional patterns and relationships. Kartachiltonia moodyi gen. nov., sp. nov., a spring-associated species endemic to the island, was discovered and populations of three additional mainland species (Austrochiltonia australis, A. dalhousiensis and A. subtenuis) were examined. The island populations of A. australis, A. dalhousiensis and A. subtenuis were found to form natural groups with differing haplotype coalescence times dating from the Early to Mid-Pleistocene. Numerous cycles of regional climate change throughout the Pleistocene are likely to have driven speciation in chiltoniid amphipods in southern Australia and the presence of multiple chiltoniid species at Kangaroo Island indicates that it exists at a likely convergence of species distribution patterns. Three possible hypotheses to explain the evolution and diversity of chiltoniids in southern Australia are discussed as are evidence for potential introduction and long-distance dispersal events.