Extensive genetic diversity exists in the populations of the Caucasus. Various hypotheses on its origin and evolution were tested by comparing genetic, geographic, and linguistic distances. Seventeen polymorphic loci and 107 localities were considered, and Mantel tests of matrix association were carried out. Genetic differences correlate more with linguistic than with geographic distances; but when populations are grouped by the language spoken, this correlation loses significance, whereas genetic and geographic distances between groups appear significantly associated. Hypotheses that classify North and South Caucasian languages into distinct families or that treat all North Caucasian languages as independent linguistic entities fail to account for genetic variation better than simpler models. We interpret these results as evidence for an evolutionary process in which linguistic and genetic divergence has resulted from population subdivision and from processes of elite dominance, that is, language replacement not associated with major migratory movements.