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South-western Australia is isolated from other forested regions of Australia by desert and bounded on southern and western sides by the Southern and Indian Oceans, respectively, with Westralunio carteri (Iredale, 1934) as the sole endemic freshwater mussel. Its conservation status is vulnerable. This species has a history of nomenclatural change and its systematic placement and population genetic history are largely unknown. We sampled 46 individuals from 13 sites across W. carteri's distribution and sequenced two mitochondrial genes (16S rDNA and cytochrome c oxidase subunit I) and one nuclear gene (28S rDNA). The mitochondrial haplotype networks and COI phylogenies revealed three evolutionarily significant units (ESUs): "W. carteri" I including the west coast populations, "W. carteri" II from the south and south-eastern range, and "W. carteri" III only occurring in the south-western tip of Australia. Four species delimitation methods identified two molecular operational taxonomic units supporting two distinct species ("W. carteri" I and "W. carteri" II + III). Phylogeographic patterns revealed herein confirm the historical separation of Western and Southern paleo-basins, also highlighting the isolation of the south-western extremity of the region. This underlines the need for taxonomic revision and will require a re-evaluation of W. carteri's conservation status.