Abstract: Rock scallop Crassadoma gigantea was introduced to China in 2012, and was successfully bred in 2015. It is in the stage of popularizing culture now. To understand the genetic relationships and the genetic variations among C. gigantea, Argopecten irradians, Chlamys farreri, and Patinopecten yessoensis, the whole sequences of ITS1 and 5S rDNA were sequenced after the amplification by PCR. The sequence characterization, genetic diversity, genetic distance, and phylogeny were determined by using a suite of biology softwares. Based on the sequences of ITS1, the numbers of haplotype and polymorphic sites, haplotype diversities, nucleotide diversities, and average nucleotide differences were varied from 2 to 6, 1 to 12, 0.425 to 0.800, 0.00081 to 0.00486 and 0.366 to 2.44, respectively. In addition, based on the sequences of 5S rDNA, their same genetic variation parameters varied from 2 to 5, 1 to 14, 0.533 to 0.841, 0.00108 to 0.1058 and 0.533 to 5.726, respectively. The result showed that all these four species had a low diversity level (π<0.01). Based on the sequences ofITS1 and 5S rDNA, the genetic distance were varied from 0.040 to 0.124, and 0.043 to 0.457, respectively, which demonstrated that C. gigantea appeared to be closely-related to P. yessoensis. Meanwhile, phylogeny trees of the genetic distances confirmed the genetic relatedness between C. gigantea and P. yessoensis. This work would provide basic information for future studies on germplasm resources management, as well as on the genetics and breeding strategies of C. gigantea.