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For the language families subsumed under Khoisan, see Khoisan languages.  Khoisan  (/ËkÉÉªsÉËn/ ; also spelled Khoesaan, Khoesan or KhoeâSan) is a unifying name for two groups of peoples of Southern Africa, who share physical and putative linguistic characteristics distinct from the Bantu majority of the region.arious Y-chromosome studies since confirmed that the Khoisan carry some of the most divergent (oldest) Y-chromosome haplogroups. These haplogroups are specific sub-groups of haplogroups A and B, the two earliest branches on the human Y-chromosome tree.
The Xhosa finally settled in the area that is now known as the Eastern Cape (formerly the Transkei and Ciskei) and comprises of a number of clans, the main groups being the Gcaleka, Ngika, Ndlambe, Dushane, Qayi, Ntinde and, of Khoisan origin, the Gqunkhwebe.his should tell us that the amaxhosa people interacted and in some instances inter-married with the san people for many years which is the reason why the Xhosa language is known to have strong clicks of the San and this development happened long before the arrival of the Boers in South Africa.