Abstract Archaeological evidence of human occupation in Arctic Siberia dates to at least 27,000 years before present (YBP) but the population history of these early inhabitants is not fully understood. Genetic research on contemporary indigenous Siberian populations has suggested a distinct pattern between populations from south/central Siberia and the extreme northeast Siberia. However, the picture is complicated by the fluctuations of movement by various cultural groups in the last millennium that has resulted in admixture as well as genetic drift. In order to better understand the genetic history of early humans in northern Siberia, we obtained ten human skeletal remains from four areas of the eastern Siberian Arctic, stretching from the low Yana River in the west to midstream of Bol'shaya Chukoch'ya River and Kolyma River in the east, and the Zhokhov site in the New Siberian Islands. We extracted DNA from the skeletal remains ranging from around 27,000 YBP to as recent as the 18th century AD and analyzed the mitochondrial DNA (mtDNA) control region. We successfully identified five haplotypes that include haplogroups A2 and C4. The presence of haplogroup C4 in Arctic Siberia by 8000 years ago illustrates the antiquity and widespread distribution of the maternal lineage in the region. On the other hand, haplogroup A2 is frequent among contemporary northeastern Siberian populations. Overall, the results from our ancient DNA analysis suggest maternal lineages among contemporary Siberians were present as far back as 8000 years ago in the Siberian Arctic.