Ancient Egyptian mummies from Abusir el-Meleq closer to ancient Levant people than modern Egyptians. Modern Egyptians genetically nearer to Sub-Saharan Africans. Ramesses II had Middle Eastern E-V22 haplotype, red hair, light skin, European features. Ancient Egyptian men carried Y haplogroups J and E from Middle East and Europe. Mitochondrial haplogroups M1, J, T, U in ancient Egyptians, almost no African L lineages. Ptolemaic male from site had Y E1b North African lineage and U6 mtDNA from Levantine Berbers. Site spans 3250 BCE to Roman period with elite and commoner burials. Genetic data confirmed by cemetery and tomb excavations. Ancient genomes match Egyptian Arabs, Copts, Berbers, Libyans more than Sub-Saharans. Rare genes link to King Tut, Akhenaten, Thuya. Ancient Egyptians show minimal Sub-Saharan African ancestry. Population changes in Egypt involved later Sub-Saharan admixture. Haplogroups indicate Middle Eastern and European affinities in ancients. No strictly African lineages dominate ancient samples. Modern shift reflects post-ancient gene flow from Africa south of Sahara.