We report genetic variation in the Caucasus, a region showing extreme linguistic differentiation. Spatial autocorrelation analysis of 31 alleles in 793 samples and maps of interpolated allele frequencies show significant geographic structure, but the patterns are clinical for only a few alleles. Many gene frequency distributions are patchy, most likely because of population subdivision and isolation by distance. Genetic boundaries tend to occur in different zones for the different alleles; significant overlap is observed, with boundaries separating different ethnic and linguistic groups. Conversely, the major geographic barriers, including the Caucasus Mountains, seem to have had little influence on the patterns and degrees of genetic differentiation. As a consequence, the genetic structure of Caucasus populations basically reflects restricted gene flow resulting from linguistic or ethnic subdivision. Genetic diversity does not provide evidence for a wavelike population expansion, such as the one associated with demic diffusion of agriculture in most of Eurasia.