Aboveground and belowground populations of the mosquito Culex pipiens pipiens are traditionally classified as form (f.) pipiens and f. molestus, respectively, and gene flow between forms is thought to be limited. Relatively few f. molestus populations have been found in the United States, which has hindered their study in North America. In this investigation, we used microsatellites to characterize a recently discovered population of f. molestus in Chicago, IL, and compared levels of genetic diversity and differentiation in above-ground and below-ground populations from Chicago and New York City, NY. Levels of genetic diversity were markedly lower in both f. molestus populations. Pairwise F_ST values between populations indicated that f. molestus populations were highly divergent from each other, as well as from their associated aboveground populations. The most likely number of genetic clusters depended on the number of loci used; we began with a set of 8, and reanalyzed the specimens with 17. Using a panel of 17 loci, there were 4 clusters, 1 for each below-ground population, and 1 for each pair of above-ground populations. Our findings are supportive of the hypothesis that f. molestus populations in Chicago and New York City arose from local aboveground populations.