Molecular genetic analysis of ancient human remains is mostly based on mtDNA owing to its better preservation in human bones in comparison with nuclear DNA. A study was made of mtDNA extracted from human skeletons found in graves in Yakutia, in order to determine the haplotypes and to compare them with lineages of modern populations. Ancient DNA was extracted from fragments of three skeletons of Yakut graves at At-Dabaan, Ojuluun, and Jaraama sites (dating back to the 18th century) and two skeletons of the Late Neolithic Kerdugen grave (2000–1000 B.C.). All graves were found in central Yakutia (Churapchinskii, Khangalasskii, and Megino-Khangalasskii districts of Yakutia). Five different haplotypes belonging to specific Asian haplogroups were identified. The mtDNA lineages of Yakut graves belong to haplogroups C4a, D5a2, and B5b. The results indicate the continuity of mitochondrial lineages in the Yakut gene pool in the past 300 years. The haplotypes of two humans from the Kerdugen site graves belong to haplogroups A4 and G2a/D. These haplotypes were compared with those of 40000 Eurasian individuals, including 900 from Yakutia. No exact matches were found in Paleo-Asian populations of Chukchi, Eskimos, Koryaks, and Itelmen. Phylogenetically close haplotypes (±1 mutation) were found in Yakut and Evenk populations, as well as in some populations of China and South and West Siberia.