The genus Cynomys and both of its subgenera, Cynomys (Cynomys) or black-tailed prairie dogs and Cynomys (Leucocrossuromys) or white-tailed prairie dogs, have their earliest fossil occurrences on the Great Plains (late Blancan for the genus and early Irvingtonian for both subgenera). However, the fossil record of prairie dogs is poor prior to the late Irvingtonian. Geographic distributions of the two subgenera during the late Irvingtonian and Ranchola-brean were consistently different from Recent distributions. Cynomys (L.) niobrarius was widely distributed across the northern and central Great Plains and commonly co-occurred with the Cynomys (C.) new sp.-C. (C.) ludovicianus lineage on the latter. In contrast, the Cynomys (C.) new sp.-C. (C.) ludovicianus lineage lived in the central and southern Great Plains, but never further north. Both subgenera, represented by C. (L.) gunnisoni and C. (C.) ludovicianus, lived in the southern highlands of New Mexico during Wisconsin time. The Mexican black-tailed prairie dog, C. (C.) mexicanus, also may have lived in southern New Mexico during Wisconsin time. Biogeographic stability on the Great Plains throughout the late Irvingtonian and Rancholabrean suggests that glacial-interglacial fluctuations in climate and habitat were not sufficient to disrupt characteristic Pleistocene distribution patterns of Cynomys prior to the Holocene.