Ethiopians and Khoisan share African-specific Groups I and II with different haplotypes. Most Ethiopians and all Senegalese belong to Group III out-of-Africa precursor. Ethiopian Y-chromosomes in Groups VI, VIII, IX trace to Asian back-migrations. Hierarchical analysis used 30 biallelic markers on 126 Ethiopians and 139 Senegalese. Study confirms archaeological and prior genetic Ethiopian-Khoisan ancestral affinity. Senegalese show no deepest clades. Ethiopians retain basal human Y-lineages Khoisan also carry. Group III dominates non-Ethiopian Africans in sample.