ITS2 (Internal Transcribed Spacer2) region and 5.8S, partial 28S of ribosomal DNA was PCR amplified and sequenced in Chlamys farreri, Mizuhopecten yessoensis. For each species, two clones were examined. Alignment of sequence suggested the presence of ITS2 with 272 –286 bp respectively, 5.8S with 155 bp. Both entire 5.8S and partial 28S with 118 bp in length were 100% homologous and ITS2 were responsible for sequence variation between the two pieces while ITS2 was 100% homologous within intraindividual Chlamys farreri and 96.5% homologous within intraindividual Mizuhopecten yessoensis. Presence of sequence variation in the ITS region suggested that it could be used for assaying genetic diversity in scallops. These results provide new insights into precise identification of relationships between scallop species.