Sixty-one autosomal non-coding regions of DNA were analyzed in samples of three sub-Saharan populations: the Biaka (Pygmies of Central Africa), San (hunter-gatherer peoples of Southern Africa) and Mandenka (farmers of West Africa). A demographic model was used comparing the null hypothesis (no archaic admixture) with the alternative hypothesis (minor archaic admixture). Two scenarios were examined: "two-population" (two modern populations) and "three-population" (an additional archaic population), using a coalescent approach and haplotype statistics (including S*). The simulations unequivocally rejected the hypothesis of no admixture and indicated that about 2% of the genome of modern Africans came from an archaic population that separated from the Homo sapiens lineage about 700,000 years ago, and these genes were introduced into the population pool about 35,000 years ago. Analysis of the three-population model revealed two scenarios: a main one with T₀≈700 thousand years ago, Tₐ≈35 thousand years ago and a≈2% share, and a side one with T₀≈375 thousand years ago, Tₐ≈15 thousand years ago and a≈0.5% . For T₀, a 95% CI of 125 thousand -1.5 million years was calculated (with Tₐ<70 thousand years). Three candidate locus (4qMB179, 13qMB107, 18qMB60) with deep haplotype separation and unusual coupling relationship (LD) structure were identified, suggesting the archaic origin of these fragments. At the 4qMB179 locus, a segment was found ca. 31.4 kb with a strongly divergent haplotype, present mainly in the pygmy Biak population . The length and structure of this block (ends in recombination hotspots) indicate that it is a relic of an archaic DNA segment. Archaic haplotypes are found primarily in pygmy and South African populations. For example, haplotype 13qMB107 reaches about 12% frequency in the San (and about 15% in Mbuti Pygmies) . Notably, the Mbuti Pygmies are the only of the studied groups to carry all three identified archaic haplotypes , suggesting that the archaic population originated in Central Africa.Conclusions and Significance of the Discovery The results suggest that modern sub-Saharan populations have a small proportion of DNA from extinct hominins. The polymorphisms discovered are from a population that split from the Homo sapiens lineage in the Lower/Middle Pleistocene. Just as Neanderthal admixture was detected in Eurasians, Africans inherited genes from local archaic forms. This means that the genetic pool of Africans is a mosaic of many ancestral lineages