The definition and phylogenetic placement of the autogenous molestus form of Culex pipiens has puzzled entomologists for decades. Renewed research efforts involving this mosquito stem from its unresolved relationship to sister taxa Cx. p. pipiens [L.] and Cx. p. quinquefasciatus Say, and its undefined role in arbovirus transmission. We investigated sequence variation in numerous mitochondrial, nuclear, and rDNA genetic markers from colony and field-collected Cx. p. pipiens and Cx. p. molestus Forskål, and were unable to identify consistent differences in all but one of the markers examined. We identified genetic differences between Cx. p. pipiens and Cx. p. molestus in the Cx. p. pipiens – specific SH60 fragment described by Crabtree et al. (1997). SSCP analysis of this fragment demonstrated a high degree of polymorphism within and among individual Cx. p. pipiens compared to greatly reduced diversity in Cx. p. molestus. Cloning and sequencing of this marker revealed that individual Cx. p. pipiens contained as many as three unique SH60 variants, with some common variants shared among individuals from distant locations. In contrast, Cx. p. molestus individuals had a single SH60 variant that was also found in corresponding above ground Cx. p. pipiens populations. These results together with supporting microsatellite Wolbachia infection data support the hypothesis that independent genetic bottleneck events may have occurred through which Cx. p. molestus populations were founded from local above-ground Cx.pipiens complex.