Meretrix lusoria supports an important shellfish fishery distributed around Japan and the southern coast of Korea. The species is considered to be either local extinct or endangered in Japan and in response to a decrease in availability in Japan, M. petechialis, a closely related species, has recently been imported from China and the Korean Peninsula. M. petechialis is currently defined as an "alien species" in Japan, has been released into habitats where the local species M. lusoria occurs. We conducted a survey and detected natural hybrids between M. lusoria and M. petechialis. Nineteen Meretrix spp. population samples were collected in Japan, China, and Korea from 2004 to 2006 (15 samples from Japan, two from China, and two from South Korea). Polymerase chain reaction-restriction fragment length polymorphisms in the cytochrome c oxidase subunit I region after HincII digestion and amplification of the nuclear gene ANT enabled identification of the two species. The exotic M. petechialis was found in Yoshinogawa and Kanonji, where periodically, large numbers of M. petechialis seedlings have been released. Combined results of RFLP and ANT individual genotypes suggest the existence of at least one hybrid individual and two putative hybrids between the Japanese local species M. lusoria and the continental alien species M. petechialis found in Chichibugahama and Kanonji. This is the first record demonstrating the existence of the alien species M. petechialis and of hybrids co-occurring with local M. lusoria in a natural habitat. Our results show that the alien species M. petechialis is currently relatively rare in Japan. If however, M. petechialis populations expand in the wild, they could replace the local M. lusoria and cause genetic disturbance via hybridization, as observed at one site (Kanonji, Kagawa Pref.). To conserve the endangered local M. lusoria resource, immediate controls of the release of M. petechialis will be necessary to prevent this species spreading and hybridizing with the native M. lusoria population.