Nineteen mtDNA samples from osseous remains found in the Ust-Ida I burial ground (middle Angara River) were analyzed. An ancient population dated back to 4020-3210 B.C. by radiocarbon (14C) analysis and archeologically assigned to the Neolithic Isakovo culture of the Baikal region was described in terms of molecular genetics. Data on restriction-site polymorphisms in fragment 16,106-16,545 of the mtDNA D-loop were obtained for seven restriction endonucleases. On the basis of these data, the mitotypic structure and nucleotide diversity of the ancient population were determined. The molecular genetic characteristics of the Neolithic population were compared to the modern populations of Siberia, Mongolia, and Urals. The data obtained indicate that the studied Baikal Neolithic population was ancestral for the modern indigenous Siberian population. The time of divergence of the three regional populations (5572 years ago) was estimated from the genetic distances between the Neolithic and modern Siberian populations, assuming that the average rate of nucleotide substitution was constant. This estimation agrees with the results of the radiocarbon dating (5542-5652 years ago). The fact that the studied samples were 14C-dated allowed the rate of nucleotide substitution in the studied region of mtDNA D-loop to be directly determined.