Class Bivalvia is a group of marine and freshwater molluscs with laterally compressed bodies enclosed by a shell in two hinged parts. Bivalves have been an important source of food for humans. Clams, oysters, ark clams, scallops, cockles and mussels are the most commonly consumed kinds of bivalve, and are eaten raw or cooked. Mactridae, also known as trough shells or duck clams, is an important family of marine bivalve clams of the order Veneroida. Mactridae currently includes about 350 recognized species distributed in the world. Coelomactra antiquata (Bivalvia: Veneroida: Mactridae) was widely distributed along the Chinese coast, north to Dalian city (Liaoning province) and south to Beihai city (Guangxi province), which was most abundant in Fujian province 20 years ago. C. antiquata is one of the valuable and a promising new candidate for aquaculture, and it had been ranked as critically endangered species in China. The research results from morphology and molecular (nuclear DNA and mitochondrial DNA sequences) showed that Fujian (Zhangzhou and Changle) C. antiquata undergone significant differentiation, and it may be a subspecies of C. antiquata or a cryptic species. Comparative mitochondrial genomic analyses also showed that the differentiation between the Zhangzhu(zz-) and Rizaho (rz-)mtDNA reached the species level. The data above mentioned provide an important background to determine the taxonomic status of Zhangzhou C. antiquata. However, the evidences to determine the taxonomic status based on the current data are insufficient. The variation of NADH dehydrogenase subunit 5 gene (nad5) is larger than 16S rRNA gene and cytochrome oxidase subunit 1 gene, the nad5 differences among different populations can provide more convincing evidence for identifying the differentiation level of Fujian C. antiquata. In this study, NAD5 gene fragments of 73 samples were amplified, including four wild populations of C. antiquata (Rizhao, Lianyungang, Beihai and Zhangzhou) and each population of two Mactra species (M. veneriformis and M. chinensis). Then sequenced and 480bp nucleotide sequences of each sample were obtained. Single Nucleotide Polymorphism (SNP) analyses were done to assess the difference level between Zhangzhou and non-Zhangzhou (Rizhao, Lianyungang and Beihai) C. antiquta. Results: A total of 44 haplotypes (Haps) were detected from 73 sequences, including 29 Haps from C. antiquata four populations, 10 Haps from M. veneriformis and five ones from M. chinensis. There are significant different haplotypes between Zhangzhou and non-Zhangzhou groups. Four C. antiquata populations were divided into two groups: non-Zhangzhou group (GP1) and Zhangzhou group (GP2). There are significantly different (P < 0.01) on the content of T, A, G between GP1 and GP2. The ratio of intergroup (between GP1 and GP2) and intragroup(GP1 or GP2)nucleotide differences is 25.1-41.8. The ratio of interspecies and intraspecies (M. chinensis and M. veneriformis) differences is 24.4-36.7. Difference between GP1 and GP2 reaching the interspecies differences level of M. veneriformis and M. chinensis. The genetic distance among Rizhao, Liangyungang and Beihai populations is ranging between 0.009 and 0.012. AMOVA analysis shown that Zhangzhou C. antiquata undergone significantly high genetic differentiation (F_ST=0.966-0.978, P < 0.01). This study suggests that Fujian Zhangzhou C. antiquata have already differentiated into a new species.