Africans show archaic introgression from a population that split before Neanderthals and modern humans. Site frequency spectra confirm 2-19% archaic ancestry in four sub-Saharan populations. Yoruba genomes contain 482 megabases of archaic sequence. Mende genomes contain 502 megabases of archaic sequence. Method identifies archaic segments without reference genomes. High-frequency archaic segments indicate adaptive introgression. Archaic ancestry substantially shapes present-day African gene pools. Introgression complements Neanderthal/Denisovan admixture outside Africa. 405 whole-genome sequences analyzed from sub-Saharan groups. Ghost archaic diverged prior to Neanderthal-modern human split.