Genetic variation for seven variable loci and morphometric variability for 17 cranial characters were analyzed for black-tailed prairie dogs (Cynomys ludovicianus) within and between populations in eastern New Mexico. Significant genetic differentiation was found for prairie dogs from populations in close proximity as well as for those from distant parts of their range. The degree of local differentiation of allele frequencies and cranial dimensions was greater than that among regions separated by major geographical barriers. Genetic and morphologic associations between prairie dogs from different populations were not in agreement with proposed taxonomic classifications. Phenetic relationships between samples were not significantly associated with those for electrophoretic data. However, the amount of morphometric variability accounted for by differences among samples within four physiographic regions and that among the regions was virtually identical as that measured by electrophoretic data. Significant heterogeneity of allele frequencies was found for prairie dogs from different wards within a population, and for those from different coteries within the wards. The social behavior of prairie dogs has resulted in genetic differentiation over small distances and inbreeding and genetic drift within the social units.