The taxonomy of the Culex pipiens complex remains a controversial issue in mosquito systematics. Based on morphologic characters, 2 allopatric taxa are recognized, namely Cx. pipiens (including the form "molestus") in temperate areas and Cx. quinquefasciatus in tropical areas. Here we report on variability at the nucleotide level of an acetylcholinesterase gene in several strains and natural populations of this species complex. Few polymorphisms were found in coding regions within a subspecies but many polymorphisms were observed between subspecies in noncoding regions. We describe a method based on a restriction enzyme polymorphism in polymerase chain reaction-amplified DNA, in which the presence or absence of one restriction site discriminates Cx. pipiens, Cx. quinquefasciatus, and their hybrids. This technique reliably discriminates mosquitoes from more than 30 worldwide strains or populations. Polymerase chain reaction amplification of specific alleles may also be a useful tool for characterizing specific alleles of each sibling taxon.