The human mitochondrial genome, although small in size, shows a high level of variation that differs across nucleotide groups. In this work, mutation rates in mtDNA were compared in species of the Homo genus, including humans, Neanderthals, Denisova hominins, and other primate species. It was found that more than half (56.5%) of the polymorphisms in protein-coding genes of human mtDNA are actually reverse mutations to the pre-H. sapiens state of the mitochondrial genome. Among hypervariable nucleotide positions, only a small portion of mutations are specific to H. sapiens, while the majority of mutations (both nucleotide and amino acid substitutions) result in a loss of Homo-specific variants of polymorphisms. Most commonly, polymorphism variants specific to H. sapiens arise as a result of unique forward mutations and disappear mainly due to multiple reverse mutations, including those in mutational hot spots.