Historical sources and archaeological data predict significant population variability in mid-Holocene northern Africa. Multivariate analyses of crania demonstrate wide variation but also suggest an indigenous craniometric pattern common to both late dynastic northern Egypt and the coastal Maghreb region. Both tropical African and European metric phenotypes, as well intermediate patterns, are found in mid-Holocene Maghreb sites. Early southern predynastic Egyptian crania show tropical African affinities, displaying craniometric trends that differ notably from the coastal northern African pattern. The various craniofacial patterns discernible in northern Africa are attributable to the agents of microevolution and migration.