Reconstructing pathways of invasion is a necessary step in determining the environmental and evolutionary factors responsible for invasion. Historical and observational data have traditionally been used to infer routes of invasion, but the “silent” nature of invasions render these approaches incomplete at best. In contrast, population genetics allows the detailed reconstruction of invasion routes over extended temporal and spatial scales. We employed mitochondrial DNA sequences to test the hypothesised New Zealand origin of Australian Potamopyrgus antipodarum populations. Potamopyrgus is an invasive aquatic snail of global significance, having invaded waters in Europe, Australia, Asia and North America. Australian populations are generally considered to be the result of accidental introduction from New Zealand, with anglers, wading birds and commercial fishing stocks all regarded as potential dispersal vectors. To examine sources and pathways of Potamopyrgus invasion we sampled 16 native sites and 13 invaded sites, sequencing a region of the mitochondrial COI gene. The resulting phylogeographic structure allowed the identification of distinct COI clades and the inference of potential origins of Australian Potamopyrgus populations. We discuss the patterns of genetic structure and implications for theories relating to the routes and vectors of Potamopyrgus invasion. Finally, we consider how detailed knowledge of invasion pathways may be used to contribute to the control and prevention of biological invasions.