Pleistocene glaciations had significant effects on the distribution and evolution of arctic species. We focus on these effects in Nearctic Beringia, a high-latitude ice-free refugium in northwest Canada and Alaska, by examining variation in mitochondrial cytochrome b (Cytb) sequences to elucidate phylogeographic relationships and identify times of evolutionary divergence in arctic ground squirrels (Spermophilus parryii). This arctic-adapted species provides an excellent model to examine the biogeographic history of the Nearctic due to its extensive subspecific variation and long evolutionary history in the region. Four geographically distinct clades are identified within this species and provide a framework for exploring patterns of biotic diversification and evolution within the region. Phylogeographic analysis and divergence estimates are consistent with a glacial vicariance hypothesis. Estimates of genetic and population divergence suggest that differentiation within Nearctic S. parryii occurred as early as the Kansan glaciation. Timing of these divergence events clusters around the onset of the Kansan, Illinoian, and Wisconsin glaciations, supporting glacial vicariance, and suggests that S. parryii survived multiple glacial periods in Nearctic Beringia. Across the Arctic, Beringia has been identified as an important regional refugium for a number of species. Within Nearctic Beringia, genetic differentiation across populations of arctic ground squirrels further reflects the effect of glacial patterns on a finer scale. The arctic ground squirrel has had a long evolutionary history in the Nearctic, with strong phylogeographic structure and stable clades persisting through multiple glacial cycles.