Mitochondrial DNA (mtDNA) haplotype diversity was determined for 63 Chibcha-speaking Kuna Amerinds sampled widely across their geographic range in eastern Panamá. The Kuna data were compared with mtDNA control region I sequences from two neighboring Chibchan groups, the Ngöbé and the Huetar; two Amerind groups located at the northern and southern extremes of Amerind distribution, the Nuu-Chah-Nulth of the Pacific Northwest and the Chilean Mapuche; and with a single Na-Dene group, the Haida of the Pacific Northwest. The Kuna exhibited low levels of mitochondrial diversity as had been reported for the other two Chibchan groups and, furthermore, carried only two of the four Amerind founding lineages first reported by Schurr and coworkers (Am. J. Hum. Genet. 1990; 46: 613-623). We posit that speakers of modern Chibchan languages (henceforth referred to as the Chibcha) passed through a population bottleneck caused either by ethnogenesis from a small founding population and/or subsequent European conquest and colonization. Using the approach of Harpending et al. (Curr. Anthropol. 1993; 34: 483-496), we estimated a Chibchan population bottleneck and subsequent expansion approximately 10,000 years before present, a date consistent with a bottleneck at the time of Chibchan ethnogenesis. The low mtDNA diversity of Kuna Amerinds, as opposed to the generally high levels of mtDNA variation detected in other Amerind groups, demonstrates the need for adequate sampling of cultural or racial groups when attempting to genetically characterize human populations.