To examine the partitioning of genetic variation within the Mexican vole (Microtus mexicanus), we analyzed variation within the cytochrome b (cytb, ca. 953 bp) from 44 samples of the Mexican vole from the mountains of the southwestern United States and Mexico. Phylogeographic analyses demonstrated strong support for a western clade and an eastern clade, corresponding to the Sierra Madre Occidental and mountains of the southwestern United States (western clade) and the Sierra Madre Oriental and the Sierra Madre del Sur (eastern clade). Levels of genetic distinctiveness among vole populations in Mexico and the southwestern United States support recognition of the Mogollon vole (Microtus mogollonensis). Estimates of lineage divergence suggested an older divergence for populations in Mexico and a more recent divergence for the presumptive M. mogollonensis. Ecological analyses demonstrated a distinct climate niche between vole lineages in the Southwest and Mexico, which indicated the possible role of environmental variation in diversification of the Mexican vole. A similar pattern of climatic separation was also demonstrated between clades of the codistributed taxa Sigmodon hispidus, Neotoma mexicana, and Peromyscus truei, suggesting a broader role for climatic variation in the origin and maintenance of the region's biodiversity.