Africa has a uniquely rich cattle diversity with about 150 known cattle breeds or populations comprised of Bos indicus, Bos taurus, and their crosses. Various studies investigated their diversity and adaptation. However, meth- ods that efficiently capture genetic differences and evolution between such populations are lacking. Here, we built whole-genome ancestral recombination graphs encoded via tree sequences to describe the genomic evolution of 193 African indigenous cattle from 15 breeds – Baoule, Gourounsi, Kuri, Logone, Boran, Ghanaian shorthorn, Guinean N’dama and Nigerian N’dama from Bos taurus origin; Zebu Gobra, Zebu Maure, Baggara, Butana and Kenana from Bos indicus origin; and one Bos indicus X Bos taurus, Djakore. Our results revealed the unique diversity, genomic evolution and subspecies differentiation of African indigenous cattle. The findings from this study will pave the way for future biological discovery and more informed breeding especially in admixed cattle populations
