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Background  The  Culex pipiens  complex consists of several morphologically similar, closely related species. In the United States,  Cx. pipiens  L. is distributed North of 39° latitude, while  Cx. quinquefasciatus  Say occurs South of 36° latitude; a hybrid zone occurs between these two latitudes including in the Central Valley of California. Members of the  Cx. pipiens  complex and their hybrids are vectors for West Nile virus (WNv). Hybrid offspring of  Cx. pipiens  and  Cx. quinquefasciatus  have been found to have enhanced transmission rates of WNv over those of pure populations of each species. We investigated whether hybrids of  Cx. pipiens  and  Cx. quinquefasciatus  occurred more frequently in any of five habitats which were dairies, rural, suburban, and urban areas, and wetlands. In addition, the proportion of alleles unique to  Cx. quinquefasciatus  and  Cx. pipiens  found in each habitat-associated population were determined.    Methods  Amplified fragment length polymorphism (AFLP) markers were used to compare the population structure of the  Cx. pipiens  complex from each habitat to geographically distant populations considered pure  Cx. pipiens  and  Cx. quinquefasciatus . Structure analyses were used to assign individuals to either  Cx. pipiens ,  Cx. quinquefasciatus , or hybrids of the  Cx. pipiens  complex. The ancestry of hybrids (F1, F2, or backcrossed) in relation to the two parent populations was estimated for each Central Valley population. Loci unique to the pure  Cx. pipiens  population and the pure  Cx. quinquefasciatus  population were determined. The proportion of loci unique to  Cx. pipiens  and  Cx. quinquefasciatus  populations were subsequently determined for each population from the five Merced habitats and from the Oroville California population. The unique loci found in Merced populations and not in  Cx. pipiens  or  Cx. quinquefasciatus  were also determined. A principal components analysis was run, as was an analysis to determine loci under putative selection.    Results  The Structure Harvester analysis found K = 3, and the  Culex pipiens  complex mosquitoes formed a genetic cluster distinct from  Cx. quinquefasciatus  and  Cx. pipiens . Individuals collected from each habitat were nearly all hybrids. However,  Cx. pipiens  complex collected near dairies had more individuals categorized as  Cx. pipiens  than collections from the other habitats. None of the mosquitoes collected in Merced or Oroville were considered pure  Cx. quinquefasciatus . Significant genetic divergence was detected among the  Cx. pipiens  complex from the five habitats in Merced;  Cx. pipiens  complex mosquitoes from dairies were divergent from the urban and suburban populations. New Hybrids analysis found that individuals from all five Merced habitat-associated populations and the population from Oroville were primarily categorized as hybrids backcrossed to the  Cx. pipiens  population. Finally, all five habitat-associated populations shared more alleles with  Cx. pipiens  than with  Cx. quinquefasciatus,  even though the pure  Cx. quinquefasciatus  population was more geographically proximate to Merced. Results from the principal component analysis, and the occurrence of several unique loci in Merced populations, suggest that  Cx. pipiens molestus  may also occur in the habitats sampled.    Conclusions  Nearly all mosquitoes in the five habitats in Merced in the Central Valley of California area were hybrids of  Cx. pipiens  and  Cx. quinquefasciatus , consisting of hybrids backcrossed to  Cx. pipiens.  Habitat-associated mosquitoes collected near dairies had more individuals consisting of pure  Cx. pipiens , and no mosquitoes from Merced or Oroville CA classified as pure  Cx. quinquefasciatus . The genetic distances among  Cx. pipiens  and  Cx. quinquefasciatus , and hybrid populations agree with previous studies using other molecular markers.  Cx. pipiens  hybrids in Merced shared more alleles with  Cx. pipiens  than  Cx. quinquefasciatus  which was unexpected, since Merced is geographically closer to the northern limit of  Cx. quinquefasciatus  distribution.  Culex pipiens molestus  may occur in more habitats in the Central Valley than previously suspected, which warrants further investigation. Future studies could investigate the vector competence of hybrids backcrossed to either  Cx. pipiens  or  Cx. quinquefasciatus  parent for their ability to transmit West Nile virus.    Electronic supplementary material  The online version of this article (10.1186/s13071-017-2594-6) contains supplementary material, which is available to authorized users.

Population genetic structure of the Culex pipiens (Diptera: Culicidae) complex, vectors of West Nile virus, in five habitats