Southern African Bantu-speaking negroid and San populations were examined with regard to the glucose-6-phosphate dehydrogenase (G6PD) PvuII restriction fragment length polymorphism (RFLP) showing alleles of 4 kb and 1.6 kb, called Type 1 and Type 2, respectively. The standardized disequilibrium coefficient for the electrophoretic G6PD types and PvuII alleles in the Southern African population was 0.28. The molecular lesion causing the GdA mutation is the same in the San and Southern African negroid populations. GdA chromosomes are found in association with both the Type 1 and Type 2 alleles, whereas none of the 62 GdB chromosomes from the Southern African populations had the Type 2 allele. Five of the 44 GdB chromosomes studied in the American Black population had the Type 2 allele, indicating that the GdB allele in the two populations may have different origins. The presence of all 3 A- deficiency mutations in the G6PD A gene, in a region where the ancestral population was thought to have predominantly G6PD B, may be explained by their origin in Africa after the divergence of the races.