We developed eight microsatellite markers using high-throughput pyrosequencing and screened these in two species (82 individuals) of threatened New Zealand land snails from the genus Powelliphanta. The taxa examined included five of the seven subspecies of P. Lignaria, in addition to its sister species, the newly described P. augusta. We also sequenced part of the cytochrome c oxidase subunit I gene for these taxa. Powelliphanta augusta is differentiated from its sister species P. Lignaria at both mitochondrial DNA and microsatellite loci. Of the five P. Lignaria subspecies we sampled, only one formed an exclusive genetic cluster based on Bayesian clustering of microsatellite data. None of the P. Lignaria subspecies was monophyletic for mitochondrial DNA. We are unable to determine if the lack of genetic differentiation is the result of hybridization, as hypothesized by previous authors, or very recent differentiation. Our data cast doubt on the current classification of subspecies within P. Lignaria and suggest that further scrutiny of the current morphological characters used to differentiate these subspecies is warranted. We recommend that conservation strategies be based on genetically defined groups identified through analysis of multiple nuclear markers rather than the existing taxonomic subspecies of P. Lignaria.