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The variation of 77 biallelic sites located in the nonrecombining portion of the Y chromosome was examined in 608 male subjects from 22 African populations. This survey revealed a total of 37 binary haplotypes, which were combined with microsatellite polymorphism data to evaluate internal diversities and to estimate coalescence ages of the binary haplotypes. The majority of binary haplotypes showed a nonuniform distribution across the continent. Analysis of molecular variance detected a high level of interpopulation diversity (Φ_ST=0.342), which appears to be partially related to the geography (Φ_CT=0.230). In sub-Saharan Africa, the recent spread of a set of haplotypes partially erased pre-existing diversity, but a high level of population (Φ_ST=0.332) and geographic (Φ_CT=0.179) structuring persists. Correspondence analysis shows that three main clusters of populations can be identified: northern, eastern, and …