Six populations of Sinonovacula constricta came from Yueqing Bay, Zhejiang and other five populations from Jiangsu and Fujian Provinces. Based on the morphologic data, the population from Fujian Zhuta is more similar to five wild populations of Yueqing Bay; The mean of discrimination accuracy of 11 populations is 82.4%, the eigenvector-loading values from Front-end of dorsal to Front-end of dorsal, from Front-end of dorsal to Back-end of dorsal, and from Beak to Anterior of body are higher than other parameters, and they all are the important to distinguish populations. SRAP analysis on 11 populations shows the genetic diversities of wild populations from Yueqing Bay are relatively high with mean Shannon's index 0.481 4, and the mean Shannon's index of other populations is 0.402 8; All six populations from Yueqing Bay gathered into one branch. Together, the morphology and SRAP both showed that the wild populations of Yueqing Bay were more highly similar.