In 1907, two mummies were discovered in Deir Rifeh Egypt in a tomb belonging to a governor and his sons from the 12th Dynasty (almost 4000 years ago). The tomb group is one of the best preserved and best known burials of the Egyptian Middle Kingdom. Although the mummies were heavily decayed, the skeletons were still preserved. Khnum-Nakht was about 40 years old and Nakht-Ankh about 60.

The two mummies were found to be brothers with the same mother but different fathers. This is confirmed by identical mtDNA and the detected differences in the Y chromosomes. Both suffered from osteoarthtritis and dental attrition. Khnum-Nakht had kyphoscoliosis and Nakht-Ankh had lung lesions from sand pneumoconiosis.

The Late Period of ancient Egypt lasted from 664 BC to 332 BC. The Pre-Ptolemaic sample JK2134 is an Egyptian Priest of Osiris, buried in the same tomb complex as Iufaa, an Egyptian priest and administer of palaces. Iufaa's mummy was discovered in an unmolested tomb in 1998 which had a white limestone sarcophagus filling the main chamber and represented the first unrobbed shaft tomb since 1941. The tomb contained stone vessels, wooden furniture, pottery and papyrus scrolls. Some of the pottery was from the Aegean and the walls of the tomb were covered with texts from the Book of the Dead.

The Ptolemaic dynasty was established by Alexander the Great's Macedonian general Ptolemy I Soter. Alexandria became the capital and center of trade. The Ptolemies named themselves as pharaohs. The Greeks and the Romans who entered by the north dominated Egypt. The Ptolemaic mummy is from this period. DNA analysis shows light skin and a male haplogroup which is common to southeastern Europe. Cleopatra is also from this time period and descended from Ptolemy I Soter. Her native language was Koine Greek and she was the first Ptolemaic ruler who learned the Egyptian language.