We used eight highly polymorphic molecular markers (microsatellites) to characterize the extent of the hybridization between Culex pipiens (both forms) and Cx. quinquefasciatus in the US. We examined populations from three longitudinal transects, two on the East coast and one on the West Coast. The markers used were chosen based on three criteria: (1) a sufficient number of markers were needed to insure statistical accuracy during the analyses; (2) the markers had to be amplifiable in all taxa (3) the markers had to include alleles unique to each taxa, allowing a clear separation between the genomes of pure populations and those of potential hybrids. We obtained specimens of Cx. pipiens complex by contacting entomologists in local Departments of Health, Vector Control Units, and Universities. We found much deeper introgression of alleles from each species than expected from previous classical analysis of male genitalia. A Bayesian multilocus cluster analysis without a priori identification of the specimen's geographical origin identified three distinct microsatellite signatures. We found virtually no individuals with a “pure” signature in the mid-latitudinal states, and found that the frequency of hybrid types shifts across elevation, at each latitude, likely associated with temperature. We examined how temperature may affect hybrid distribution by performing laboratory studies and developed a predictive model of the impact of hybridization on the population dynamics of Culex pipiens complex across the US latitudinal gradient.