To provide empirical evidence of species boundaries and the role of climatic change in affecting evolution, we documented evolution of the sagebrush vole, Lemmiscus curtatus, through hundreds of thousands of years by following populations from the middle Pleistocene to the present. We found that: (i) extant representatives of the species culminate a morphological transition that was initiated within an unusually arid and warm interglacial period, perhaps related to the shift from glacial-interglacial cycles dominated by a 41,000 year periodicity to those dominated by a 100,000 year rhythm; and (ii) sympatry of extant and extinct morphotypes persisted for more than 800,000 years. This exceptionally detailed tracing of extinct populations into extant ones suggests that species such as the one we studied are real entities in space, that their boundaries become fuzzy (although potentially diagnosable) through time and that unusual climatic warming may initiate significant evolutionary change manifested at the morphological level.