H2 haplotypes show patchy distribution across Africa. North Africans display higher frequency of inverted H2 subtypes than Sub-Saharans. North African H2 chromosomes are genetically closer to non-African ones. This supports North Africans diverging more recently from non-African groups. H2 family shows higher diversity than previously known. Diversity weakens evidence for strong selective sweep on all inverted chromosomes. Locus has complex evolutionary history. Sub-Saharan groups have lower inverted subtype frequencies. Population stratification reveals distinct H2 subtypes by region. Phylogenetic analysis links North African H2 to non-Africans.