The notoriously fragmented nature of the chiropteran fossil record has made it extremely difficult to resolve issues of evolutionary history based solely on morphological data. Placing estimates on dates of divergence for taxa, as well as developing a reliable calibration for a molecular clock, has been problematic due to a deficiency in reliable fossil calibration points, and a lack of statistical power in the analyses available, as well as the mistreatment of the available data. We obtained sequence data from the hypervariable D-loop of the mitochondrial DNA control region of Corynorhinus rafinesquii, C. mexicanus, and the five recognized subspecies of C. townsendii and employed a relaxed molecular clock model to test competing hypotheses of evolution for big-eared bats in North America. Our analyses indicate interspecific divergences occurred during the Pliocene, with C. rafinesquii diverging from the other Corynorhinus relatively early, during periods of increased warmth and significantly higher sea levels, and C. townsendii and C. mexicanus diverging relatively late, possibly during the cooler periods leading up to the Pleistocene. Intraspecific divergences within C. townsendii appear to have occurred as a result of repeated glacial advances during the Pleistocene, with the C. t. ingens and C. t. virginianus lineages arising at relatively the same time as C. t. pallescens and C. t. australis, and recent rapid population decline producing the disjunct distribution of C. t. ingens and C. t. virginianus. Dating and demographic analyses indicate all species of Corynorhinus are likely undergoing population decline.