There is evidence that Amerindians have continuously occupied the lower Central American Isthmus for as long as 10,000 years. There remains some doubt about the relationships of these original colonizers to the resident peoples of this zone at the time of European contact (approximately A.D. 1500). We present new genetic data for up to 48 genetic loci for 570 members of six Chibcha-speaking tribes of lower Central America--the Boruca, Bribri, Cabecar, and Guatuso of Costa Rica and the Kuna and Teribe of Panama--and delineate the genetic affinities among the various groups (these six tribes and the Guaymi and Bokota) of lower Central America. We convert standard genetic distance metrics into a form that is linear with the effective time since divergence, and we compare the genetic distances with linguistic distances for the same groups (r = .74, P less than .001). Geographic affinity accounts for some of the genetic divergence among groups (r = .49, P less than .084) and for some of the linguistic divergence (r = .53, P less than .037), but the correspondence between geographic position and taxonomic affinity is not high. We combine all of the genetic and linguistic data to construct a synthetic overview taxonomy of the lower Central American Chibcha. Both the genetic and linguistic data exhibit hierarchical organization of tribal groups, showing a general east-to-west pattern of grouping, with greater affinities between close neighbors. The presence of private genetic variants of some antiquity within the region and their absence outside the zone, coupled with the essential absence of the DI*A polymorphism of mongoloid origin that is widespread outside the zone, argue for a relatively isolated development of the Central American Chibcha. Our results do not support the old view of lower Central America as a frontier between more advanced cultures to the north and south. Any such explanation would require recent waves of migration from outside the region, migration that is not compatible with either the genetic or linguistic data or with the archaeological history of the region.