Khoisan languages of southern Africa have a putative history of considerable time depth and are spoken by Khoi and San populations. San carry the deepest known gene lineages. Intriguingly, while the Hadzane language of the Hadabe (Hadza) of East Africa shares click consonants with Khoisan, the historical relationship between these languages has remained enigmatic. Over the past century a minority of linguists has suggested that click consonants are preserved elements of human language tracing to the common ancestral population of extant humans, or earlier. Evidence supporting this hypothesis, however, has been scant. We present Y chromosome and mtDNA data indicating that San and Hadzabe are among the most highly divergent of human populations. Both DNA segments independently reveal variation consistent with the hypothesis that all living humans descend from speakers of a click language.