The occurrence of natural hybridization between the mosquitoes Culex pipiens pallens and Cx. pipiens f. molestus in Northwestern Kyushu, Japan, was confirmed based on morphology and molecular methods. In order to assess the morphological difference in male genitalia of the two forms on the basis of the dorsal/ventral (D/V) ratio, mosquito egg rafts were collected in Nagasaki City using oviposition traps. The morphological parameters of male genitalia from Cx. pipiens f. molestus were discontinuous with those from Cx. pipiens pallens, while intermediate individuals could be found in a single egg raft. These individuals were identified as hybrids using a polymerase chain reaction (PCR)-based assay. The fitness of the family descended from hybrids was lower than that from typical pallens and molestus families, as measured by egg raft size and egg hatchability. The reduced fitness of the hybrids suggested that the genetic introgression between the two forms could be restricted.