Mitochondrial 16S rRNA gene fragment of Sinonovacula constricta was amplified with polymerase chain reaction (PCR). The PCR products were purified and sequenced from three wild populations: She-yang (WS), Chong-ming (WC), Xiang-shan (WX) and three cultured populations She-yang (CS), Feng-xian (CF), Xiang-Shan (CX) in Jiangsu, Zhejiang and Shanghai. 440 base-pair nucleotide sequences of 16 SrRNA were examined and analyzed for genetic polymorphism. Sequences data analysis showed that all 47 sequences were grouped into 19 haplotypes and there were 41 variable nucleotide positions in 16S rRNA gene fragments. The genetic diversity indexes were calculated and the results indicate that the significant genetic difference was observed among three wild populations, WC population has more variation than others, followed by WS population, WX population has the least sequence variation,which suggests that WC population has not been polluted by cultured populations. But there is no genetic difference among three cultured populations and it is closest to WX population. So the culturing process has reduced wild genetic diversity.