The endemic land snail genus Wainuia (Pulmonata: Rhytididae) most likely forms a distinct clade within a larger radiation of carnivorous species in New Zealand. Species within the clade are poorly resolved on shell shape, which is the basis of existing classifications. Wainuia at some sites were recently found to subsist almost entirely on amphipods. This habit is found on both the North Island and South Island, but the relationships between these populations are unclear. In this study, we investigated the phylogenetic relationships of extant populations of Wainuia by sequencing regions of the mitochondrial 12S rRNA and cytochrome oxidase I genes. Our results enabled us to construct a phylogeny of extant populations of Wainuia and resolve several taxonomic uncertainties. Trees based on sequence data indicate that there are at least five distinct species of Wainuia. W. urnula nasuta is only distantly related to W. urnula and should be raised to full species rank. We recommend that a full taxonomic revision of Wainuia be undertaken, and that future conservation management take into account the important contribution of outlying populations to the diversity of this group. This phylogeny enables hypotheses regarding behaviour, morphology, and biogeography of this group to be further tested. For example, the habit of eating amphipods, along with associated dentition changes, appears to have evolved twice. Also, the extent of sequence divergence between these taxa does not provide evidence for a land bridge across Cook Strait in the last interglacial period, as reported previously.