All modern humans including Africans have Neanderthal ancestry. Non-Africans inherited about 2% Neanderthal DNA after leaving Africa. New IBDmix method detects Neanderthal ancestry in Africans for first time. Africans show higher Neanderthal levels than previously estimated. Europeans and Asians have roughly equal Neanderthal ancestry. Neanderthal DNA reached Africans via ancient Eurasian migrations back to Africa. Some African Neanderthal signals stem from human DNA introgressed into Neanderthals. Neanderthals and humans interbred around 50,000 years ago. Shared ancestry with Neanderthals dates to 500,000 years ago. Method distinguishes ancient shared ancestry from recent interbreeding. Limited African samples analyzed but findings spur more research. Sub-Saharan Africans previously thought Neanderthal-free. Interbreeding gave humans potential advantages over Neanderthals. Modern humans outcompeted Neanderthals leading to their extinction 40,000 years ago.