We exposed two species of shellfish, Patunopecten yessoensis and Tapes japonica, for 4 h to artificial sea water in which N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), ethyl nitrosourea (EMS), 3-chloro-4-dichloromethyl-5-hydroxy-2(H)-furanone (MX), or benzo[a]pyrene (B[a]P) were dissolved. We then assessed the DNA damage in cells isolated from the gills using the alkaline single-cell gel electrophoresis (SCG) assay. A statistically significant increase in DNA damage was observed for all exposures. Therefore, the alkaline SCG assay detected DNA damage in gill cells produced by direct mutagens and promutagen dissolved in sea water. T. japonica was exposed to sea water sampled from two Pacific Ocean coasts of Japanese local cities--Hachinohe (Aomori Prefecture, Tohoku) and Nakatsu (Oita Prefecture, Kyushu)--and three bay coasts of the industrial megalopolises--Tokyo, Osaka, and Kobe. A significant increase in DNA damage was observed after the exposure to sea water from Tokyo, Osaka, and Kobe, but not from Hachinohe and Nakatsu. These results suggested the utility of the alkaline SCG assay with shellfish gill cells for monitoring sea water genotoxicity.