Nucleotide sequences of the circadian rhythm genes, period and timeless, were studied for the first time in mosquitoes Culex pipiens Linnaeus, 1758. In this work we evaluated variations of the studied genome fragments for the two forms of C. pipiens (forma “pipiens” – mosquitoes common for aboveground habitats, forma “molestus” – underground mosquitoes). We compared C. pipiens from Russia with transatlantic C. pipiens and subtropical Culex quinquefasciatus Say, 1823. Our results show that intraspecies variability is higher for the gene period than for the gene timeless. The revealed substitutions in nucleotide sequences and especially in amino acid sequences grouped the individuals of the two forms into distinct clusters with high significance. The detected fixed amino acid substitutions may appear essential for functioning of the circadian rhythm proteins in C. pipiens, and may be correlated with adaptations of the taxa within the group C. pipiens. Our results suggest that natural selection favors fixed mutations and the decrease in diversity of the genes period and timeless in mosquitoes of the C. pipiens f. “molestus” compared with the C. pipiens f. “pipiens”, is probably correlated with adaptive features of C. pipiens f. “molestus”. The studied genome regions may be considered as promising molecular-genetic markers for identification, population and phylogenetic analysis of similar species and forms of the Culex pipiens complex.