Eisenia nordenskioldi is an earthworm widespread in Northern Asia and adjacent regions. It is known for its high morphological, karyotypic, and genetic variation, and contains two subspecies, the pigmented E. n. nordenskioldi and the unpigmented E. n. pallida. We obtained almost complete sequences of mitochondrial genomes (without the control region and parts of the flanking tRNAs) for six genetic lineages of E. n. nordenskioldi, two for E. n. pallida, as well as for three congeneric outgroups. These genomes had gene content and arrangement typical for Annelida. Nucleotide and amino acid diversity among E. nordenskioldi lineages was almost as high as between them and the outgroup species. E. nordenskioldi was split into two clades, one containing E. n. nordenskioldi lineages 6 and 9, and the other comprised the rest of the lineages. We could not resolve relationships of these two clades with E. tracta; most datasets used recovered this species as the sister group to E. n. nordenskioldi lineages 6 and 9, but not with high statistical support. According to mtDNA data, neither E. n. nordenskioldi nor E. n. pallida are monophyletic, and the same could be true for E. nordenskioldi as a whole, which suggest a revision of the systematics of E. nordenskioldi complex.