Coelomactra antiquata (Bivalvia: Mactridae) is distributed widely in the western Pacific Ocean, along the coast of Indo-China Peninsula, Japan, Korea and China. C. antiquata has a wide but erratic distribution, and is one of the most critically endangered species in China. Background genetic data are critical to successful cultivation of C. antiquata, Mitochondrial DNA (mtDNA) is widely used for genetic difference analysis among closely related species, since it accumulates mutations more rapidly than most nuclear regions. The internal transcribed spacer 2 (ITS2) of the nuclear ribosomal repeat unit is one of the most commonly applied phylogenetic markers. It is a fast evolving locus, which makes it appropriate for studies at low taxonomic levels. The present molecular study was conducted on partial sequences of the mitochondrial 16S rRNA genes (16S) and ITS2 sequence from nuclear DNA to assess genetic variations in C. antiquata. Nine wild stocks of C. antiquata were collected from Daliang (Liaonin Prov. DL), Jimo (Shandong Prov. JM), Jiaonan (Shandong Prov. JN, JD) and Rizhao (Shandong Prov. RZ), Lianyungang (Jiangsu Prov. LYG,X3) and Qidong (Jiangsu Prov. QD XM), Changle (Fujian Prov. CL, X1), Beihai (Guangxi Prov. BH) and Pingtan (Fujian Prov. X2) in China, and the coast next to China in Vietnam (YN). We analyzed 147 sequences in total: 74 from ITS2 (389-402bp) and 73 from 16S (306bp), Seventeen genotypes were detected from ITS2 sequences and 15 haplotypes were detected from 16S sequences. The Changle group (CL, YN,X2) has nine exclusive ITS2 genotypes and five 16S haplotypes. The majority of non-Changle (nCL) groups (DL, JM, JN, JD, RZ, LYG, QD, XM, BH) share one or several genotypes (or haplotypes) among groups. The ITS2 alignment for 17 genotypes contained 401 nucleotide positions (including indels) with 23 variable sites (5.7%), of which 16 (4.0%) were parsimony informative. The 16S alignment for 15 haplotypes contained 306 bp with 35 (11.4%) variable sites, of which 24 (7.8%) were parsimony informative. The average intergroup genetic distance of nCL group is 0.007. The secondary structures of 9 genotypes and 5 haplotypes of CL group were different from those of nCL group, whereas the secondary structures of ITS2 and 16S are quite similar in nCL group. The phylogenetic analysis of ITS2 and 16S gene showed that the group CL formed a monophyletic clade with a high support (BP=98, 96), whereas the group nCL formed a second separate clade also with a high support (BP=98, 96). The results of this study suggests that the C. antiquata from Fujian province may be a new species of genus Coelomactra.