Ancient diversity in Sub-Saharan Africa is known to have been re-modulated to a large extent by Bantu migrations in the sub-Sahel region, in two southwards waves of advance through both the west and east coasts. Haplotype matching performed for Y-STR haplotypes in several sub-Saharan populations, both inside and outside the migration path, allowed the confirmation of a putative founder haplotype, and its one-step neighbours, of Bantu origin, and detected an increasing drift towards the south, with a stronger reduction of diversity along the western coast. A mixed frequency distribution for the Bantu haplotype core in South Africa, relative to the western and eastern pools, seems to provide evidence for the intermingling between both Bantu waves in that region. The proportion of male lineages considered as predating the Bantu expansion reached 8.8% in Mozambique. Further influence on sub-Saharan diversity may have occurred during the colonial period; in Mozambique, the European genetic impact in the male component was estimated to be around 5.9%, in significant contrast with the female counterpart where no European lineages were detected.