Mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs) were investigated in 95 individuals, consisting of 49 San ('Bushmen') and 46 Nama ('Hottentot') individuals from Namibia, using the restriction enzymes HpaI, BamHI, HaeII, MspI, AvaII and HincII. Six of the eleven types found in the pooled Khoisan sample are shared, albeit at varying frequencies, suggesting that both the San and Nama have evolved from a recent common ancestor. However, San and Nama groups differ appreciably, in particular, type 3-2 (3-1-1-2-2-2) was found in 7/49 Sekele and 25/46 Nama (chi 2 [1] = 15.3, P = 9.17 x 10(-5)). In addition, type 4 makes up 42.8% of the types found in the San, and is not found in the Nama group. This suggests that the San and Nama have evolved along separate lineages, with little gene flow between them, following their proposed separation from a common Khoisan ancestor. Type 7-2 (3-1-1-1-1-2), most common in Negroid populations, is found at a higher frequency in the San (20.4%) than the Nama (6.5%), suggesting that miscegenation involving Negroid females and San males is more common than that between Negroid females and Nama men. The higher frequency of type 21-2 (2-1-1-1-2-2) in the Nama (13%) than in the San (4.1%), may be attributable to gene flow from the Dama into the Nama, consistent with the consequences of enslavement of the Dama by the Nama.