There is a long-standing debate over whether or not the Pleistocene glaciations promoted speciation. While some models predict that extensive mixing of populations during interglacial expansion would have inhibited divergence, others postulate that divergence among allopatric glacial refuges or founder events during recolonization of previously glaciated areas would have promoted differentiation. Using a combination of traditional and coalescent based population genetic approaches, this study finds that the glaciations did not inhibit divergence among populations of the grasshopper Melanoplus oregonensis. Instead, drift associated with recolonization of previously glaciated areas, as well as divergence among multiple allopatric glacial refugia, have both contributed to differentiation in this montane grasshopper from the ‘sky islands’ of the northern Rocky Mountains. Significant population structure was detected by phylogenetic and FST analyses, including significant FST values among individual pairs of sky-island populations. In addition to clustering of haplotypes within populations, there is some evidence of regional phylogeographic structure, although none of the ‘regional groups’ form a monophyletic clade and there is a lack of concordance between the genealogical and geographical positions of some haplotypes. However, coalescent simulations confirm there is significant regional phylogeographic structure that most likely reflects divergence among multiple ancestral refugial populations, and indicate that it is very unlikely that the observed gene tree could have been produced by the fragmentation of a single widespread ancestral population. Thus, rather than inhibiting differentiation, the glaciations appear to have promoted population divergence in M. oregonensis, suggesting that they may have contributed to the radiation of Melanoplus species during the Pleistocene.