Present-day African population structure dates to Marine Isotope Stage 5. Earliest divergence among contemporary African populations occurred 120,000-135,000 years ago. Divergence preceded by gene flow between two or more weakly differentiated ancestral Homo populations over hundreds of thousands of years. Weakly structured stem models explain polymorphism patterns previously attributed to archaic hominins in Africa. Archaic introgression models rejected. Ancestral coexisting populations predict genetically and morphologically similar fossils. Only 1-4% genetic differentiation among contemporary humans from drift between stem populations. Nama Khoe-San genomes sequenced from 44 southern African individuals. Reticulated history inferred across eastern, western, and southern African populations. Model misspecification explains variation in prior divergence time estimates.