In spite of high loss of biodiversity in landscapes converted to farmland or urban areas, a positive correlation exists between species richness and endemism and human population density at coarse spatial scales. Data representing precolonial and contemporary human population patterns in Africa were overlaid on species distribution data covering 4080 vertebrate species. Species richness tracks both the precolonial and the current human population density. Areas of high vertebrate endemism are particularly closely associated with precolonial population centres. This suggests that patterns of population growth in Africa were, more than today, governed by factors that also enhanced local species persistence and speciation. The traditional conservation focus on wilderness areas with few people, and generally rather low endemism, needs to be complemented with strategies for sustainable development in some of the densely populated areas.