Understanding how diversity is partitioned across the landscape provides perspectives on the environmental processes that have influenced the evolutionary history of organisms. We analyzed spatial demography, historical biogeography, and niche divergence of the western jumping mouse (Zapus princeps) using molecular sequence data from mitochondrial and nuclear DNA recovered from 7 of the 11 subspecies in western North America. Phylogeographic structure within Z. princeps was partitioned across 5 clades (Boreal, Northern Sierra, Southern Rockies, Southern Sierra, and Uinta). Two lineages detected in the Sierra Nevada of California (Northern Sierra and Southern Sierra) were more closely allied to Z. trinotatus than to other lineages of Z. princeps and species distribution models mirror these phylogenetic signatures by detecting wide overlap in niches for Sierran jumping mice and Z. trinotatus as compared to other Z. princeps. Four southern lineages are deeply divergent and limited to disjunct mesic and montane habitats within the xeric southwestern United States, whereas the 5th lineage is widespread, extending from Wyoming to Alaska and reflecting expansion northward following deglaciation, a common pattern in boreal mammals.