In this study we applied PCR to amplify and analyze partial sequences of mitochondrial COⅠ, 12S rRNA and ribosome 18S rRNA, 28S rRNA of five groups of Scapharca broughtonii (Jiaonan, Rongcheng, Changdao, Penglai in Shandong Province of China, and Tongyeong of Korea). In spite of the apparent genetic variation in COⅠ, 12S, 18S and 28S, the base compositions of these genes were stable. The genetic diversity of the five populations indicated the good condition of the germplasm resource of these species. Sixty-seven sequences of COⅠ, 73 sequences of 12S, 75 sequences of 18S rRNA and 75 sequences of 28S rRNA were obtained, and their lengths were 776 bp, 443 bp, 909 bp and 894 bp respectively. Sequence analysis showed that the polymorphic sites, haplotype, Hd dversity and nucleotide diversity index of COⅠ were 466, 32, 0.925 and 0.086, respectively. While that of 12S were 292, 43, 0.928, 0.0856, and 18S were 909, 74, 1.0, 0.717, and 28S were 27, 18, 0.778, 0.289. In addition, the Jiaonan population and Penglai population showed the highest diversity in 18S and 28S. Genetic distance data revealed the Korea population has bigger genetic distance with China population than that of within populations from China. Clustering analysis based on the partial sequences of COⅠ gene showed that the China S. broughtonii individuals from same population China clustered generally together, however, the Korea individuals clustered more than one group.