The genetic relationship was examined with PCR-RAPD markers among three scallop species, Chlamys farreri farreri, Patinopecten yessoensis, and Agropecten irradians. Six primers were selected from 60 primers used to compare PCR-RAPD profiles among species. All primers showed distinct RAPD band patterns between the three species. In Chiamys farreri farreri, the morphological characteristics such as shell size and color were considerably different between the two geographical populations. RAPD profile, however, showed that no significant genetic differences were found between the two geographical populations. Polymorphic alleles were observed within a population of each species. Thus, PCR-RAPD markers are useful in identifying scallop species and in understanding scallop population genetic structure.