The central Rocky Mountain region of North America lies at the biogeographic crossroads of the Rocky Mountains, Great Plains, and Great Basin. Here, we examine genetic patterns in an abundant, widely distributed, and ecologically important rodent species, the long-tailed vole (Microtus longicaudus), across this climatically and tectonically dynamic landscape. We examine patterns of genetic diversity in relation to the species' overall phylogeographic distribution using mitochondrial cytochrome-b sequences from modern, historic, ancient, and published samples. Our analyses reveal extensive genetic diversity in the central Rockies, a lack of population structure, and a lack of concordance between genetic and morphological subspecies distributions. Patterns of genetic variation in late-Holocene and modern populations are similar. We conclude that geographical features such as the Continental Divide, previously isolated glacial cover, and major rivers do not result in persistent genetic structure within the long-tailed vole. We also conclude that the central Rocky Mountain region is a zone of secondary contact for divergent mitochondrial lineages of the long-tailed vole.