Species that are rare when first described present a practical management problem because it may be unclear whether the taxon is in the final stages of an anthropogenic decline, or is naturally uncommon, and each scenario dictates a distinct approach to management. We analysed mitochondrial and microsatellite DNA data with population genetic and phylogeographic tools to distinguish between these possibilities in a rare lizard from southern New Zealand. Grand skinks, Oligosoma grande, are large rock-dwelling lizards that have a fragmented distribution consisting of a western and eastern cluster of populations separated by ca. 120 km. This distribution could result from human disturbance, pre-human climatic and vegetation changes, or both. All populations were highly genetically structured (overall FST 0.171, RST 0.235), indicating that populations were demographically independent and skinks are unlikely to expand their range without human intervention. In addition, the current fragmented distribution is likely to have both historical and recent anthropogenic elements. Two eastern populations showed evidence of being historically large (high θ mtDNA genetic diversity), although they are now small, supporting anecdotal data that grand skinks have declined in historical times. However, eastern and western populations were reciprocally monophyletic for mtDNA lineages, suggesting long independent evolutionary histories that predate the arrival of humans in New Zealand. Eastern and western populations fulfil many criteria to be considered as evolutionarily significant units, but such a classification must be balanced against addressing more immediate threats to the species' survival, such as introduced predators.