Abstract Polymorphism of the mtDNA gene COI encoding cytochrome C oxidase subunit I was studied in the mosquitoes Culex pipiens Linnaeus, 1758 and C. torrentium Martini, 1925 from sixteen locations in Russia and in three laboratory strains of subtropical subspecies of the C. pipiens complex. Representatives of this complex are characterized by a high ecological plasticity and there are significant ecophysiological differences between its morphologically similar members. The full-size DNA sequence of the gene COI spans 1548 bp and has a total A+T content of 70.2 %. The TAA is a terminating codon in all studied representatives of the C. pipiens complex and C. torrentium. 64 variable nucleotide sites (4 %) were found, fifteen haplotypes were detected, and two heteroplasmic specimens of C. torrentium were recorded. COI haplotype diversity was low  in Wolbachia–infected populations of the C. pipiens complex. Monomorphic haplotypes were found in C. p. quinquefasciatus and C. p. pipiens f. molestus. Three haplotypes were detected for the C. p. pipiens, but these haplotypes were not population-specific. On the other hand, each of the ten studied Wolbachia-uninfected C. torrentium individuals from three different populations had unique mitochondrial haplotypes. Polymorphism of the 478-bp ITS2 nucleotide sequences was similar in infected C. p. pipiens and C. p. pipiens f. molestus and uninfected C. torrentium specimens. The ITS2 genetic distance between C. p. pipiens and C. torrentium reached 12.5 %. Possible effects of Wolbachia invasion on C. pipiens populations are discussed.