We compared allozymes at 12 loci in 12 populations of six species of Meretrix: M. lusoria (Japan, Korea, and Taiwan), M. petechialis (China and Korea), M. ovum (Thailand and Mozambique), M. lyrata (China), M. lamarckii (Japan), and Meretrix sp. A (Okinawa, Japan). Our allozyme results were generally consistent with the major groupings currently recognized within the genus based on morphological characters. However, we found two cryptic or undescribed species: Meretrix sp. A from Okinawa and M. cf. lusoria from Taiwan. The shell characters of Meretrix sp. A were similar to those of M. lamarckii, but the species was genetically distinct (Nei's genetic distance D > 0.845) from all other species examined. The Taiwanese Meretrix population was morphologically indistinguishable from Japanese M. lusoria, although the genetic distance between the Taiwanese and Japanese populations showed a high degree of genetic differentiation (D > 0.386). Meretrix lusoria seedlings were introduced into Taiwan from Japan in the 1920s, and Japanese M. lusoria was previously thought to be established as a cultured stock. However, our results suggest that the Taiwanese population may represent a sibling or cryptic species of M. lusoria.