Homo erectus remains have been found in Africa, Eurasia and Southeast Asia, dating back to 2 million years (Ma), but due to their age and preservation, obtaining informative molecular data from them his been difficult. We successfully extracted ancient enamel proteins from six Middle Pleistocene H. erectus specimens, approximately 0.4 Ma, from the Zhoukoudian, Hexian, and Sunjiadong sites. Five of these specimens are males, and one is female. All specimens from all three sites share two amino acid variants. Of these, AMBN-253G is unknown and has not been seen in other human lineages, including H. erectus from Dmanisi (Georgia), Homo antecessor from Atapuerca (Spain), Denisovans, Neanderthals, and modern humans. The other variant, AMBN-273V, has been previously identified in Denisovans, where it may have been introduced through populations related to these Middle Pleistocene H. erectus. The previously unknown super-archaic segments in Denisovans and later partially passed to modern humans thus likely originated from H. erectus. Late Middle Pleistocene H. erectus may have coexisted with Denisovans in parts of East Asia, where these interactions are presumed to have occurred.