Most research on the biological effects of Pleistocene glaciation and refugia has been undertaken in the northern hemisphere and focuses on lowland taxa. Using single-strand conformation polymorphism (SSCP) analysis and sequencing of mitochondrial cytochrome oxidase I, we explored the intraspecific phylogeography of a flightless orthopteran (the alpine scree weta, Deinacrida connectens) that is adapted to the alpine zone of South Island, New Zealand. We found that several mountain ranges and regions had their own reciprocally monophyletic, deeply differentiated lineages. Corrected genetic distance among lineages was 8.4% (Kimura 2-parameter [K2P]) / 13% (GTR + I + Gamma), whereas within-lineage distances were only 2.8% (K2P) / 3.2% (GTR + I + Gamma). We propose a model to explain this phylogeographical structure, which links the radiation of D. connectens to Pliocene mountain building, and maintenance of this structure through the combined effects of mountain-top isolation during Pleistocene interglacials and ice barriers to dispersal during glacials.