Genetic studies suggest the existence of hybridization between different hominid species in Africa around 35,000 years ago, which influenced human evolution. Analysis of mtDNA and numt has shown deep divisions of mtDNA lineages in hominids during the middle Pleistocene, suggesting genetic structure and gene flow between them. Africa demonstrates the complex process of hominin evolution with a series of adaptive radiations spanning several million years that led to different morphological forms. More recently, Hammer et al. (2011) and Harvati et al. (2011) provided integrated morphological and genetic evidence of interbreeding between modern humans and unknown archaic hominins in Africa just 35,000 years ago. However, genetic evidence for hybridization between hominin lineages in the Lower and Middle Pleistocene is unknown, and direct DNA extraction from extinct African hominin lineages remains elusive. The availability of nuclear and mitochondrial genome sequences of modern humans, Neanderthals and Denisovans allows us to collect mitochondrial-derived nuclear DNA sequences (numts) inserted into the nuclear genome of ancestral hominin lineages and draw conclusions about hominin evolution in the distant past. Analysis of mtDNA and numts revealed a deep division of mtDNA lineages that existed in African hominins in the middle Pleistocene. The first cluster included human and Neanderthal mtDNA sequences, while the second consisted of DNA sequences that are known today as mtAncestor-1, a nuclear fossil mtDNA and Denisova mtDNA isolated from a bone and tooth found in southern Siberia. The two groups initially diverged 610,000-1,110,000 years ago. About 220,000 years after the original split, the Denisova mtDNA - mtAncestor-1 lines mixed with the mtDNA pool of the ancestral populations of Neanderthals and modern humans. This admixture after deep division is demonstrated by the transposition of a Denisov-like mtDNA sequence into the nuclear genome of the ancestral population of Neanderthals and modern humans. This finding suggests a matrilineal genetic structure among Middle Pleistocene hominins, as well as the existence of gene flow between African hominin lineages. Through paleogenomic analyses, the theory that population structure and gene flow in African hominins influenced the pattern of admixture observed in the nuclear genomes of non-Africans cannot be ruled out.