Samples from Middle Egypt span 1300 years from New Kingdom to Roman Period. 90 mitochondrial genomes and genome-wide data from three mummies analyzed. Ancient Egyptians cluster genetically with Near Easterners. Present-day Egyptians show additional sub-Saharan African ancestry. Sub-Saharan admixture in Egyptians occurred after ancient times. Foreign dominations in first millennium BCE increased foreigners but ancient DNA shows Near Eastern continuity. Ancient mummies provide genome-wide insight into Egypt's genetic history. Mitochondrial haplogroups analyzed in detail. Principal component analysis places ancient Egyptians with Near Eastern populations. Shared drift confirms less sub-Saharan input in ancients. Modern Egyptians diverged via recent African gene flow. Egypt's location drove interactions with Africa Asia Europe. Ancient Egyptians not genetically like today's sub-Saharan admixed population.