Quaternary climate fluctuations and topographical variation in the Pacific Northwest region of North America have interacted to affect the historical biogeography of biota in this region. High-elevation mammals have unique diversification patterns due to their isolation on mountaintops and potential for population growth and range expansion in lowland refugia that are available during glacial periods. We examined the phylogeographic structure, dates of lineage diversification, and historical demography of western heather vole (Phenacomys intermedius) populations across several mountain ranges in the Pacific Northwest. Our analysis of sequence variation in the mitochondrial control region using both maximum-likelihood and Bayesian methods identified 3 major geographically distinct lineages: an Oregon and California lineage, Washington lineage, and Northern and Interior lineage. Our estimate of divergence times using a Bayesian relaxed molecular-clock method revealed that diversification among these major lineages began ∼1.8 million years ago (mya) in the early Pleistocene with the split of the Oregon and California lineage followed by the split of the Washington lineage and the Northern and Interior lineage ∼1.5 mya. All 3 clades remain allopatric, suggesting that they did not share a common refugium during cold climatic intervals of the Pleistocene. Further diversification within each major clade occurred in the middle Pleistocene when populations in isolated mountain ranges became distinct. Demographic estimates from Bayesian skyline plots indicate that each of the 3 major clades has experienced population decline since the early Holocene, possibly due to the redistribution of populations into higher-elevation habitats that became restricted to mountaintops following continental and alpine deglaciation.