The freshwater discharge from river and ocean current system influenced the population genetic structure of marine mollusk organisms via promoting or limiting planktonic larval dispersal. The clam, Meretrix meretrix, is an important aquaculture species in the coastal regions of China. However, the previous studies of genetic information about M. meretrix were vague. None integrated research to reveal the population genetic and structure of M. meretrix in China from north to south. In this study, we investigated the genetic variation of seven location samples distributing the China coastline from north to south by mitochondrial DNA (COI and Cytb genes). The genetic diversity of seven samples was in a high level (h = 0.879-0.949, π =0.0033-0.0110). The Bayesian skyline plots showed that the samples were a stable population. The genetic divergence of seven samples was suggested that there was detected two obviously groups from pairwise FST values and networks. This differentiation was conformed to the geographic of the sampling sites. However, within the groups, the gene flow of the samples was frequency and showed non-significantly divergence. The results provided insights that the Yangtze diluting water and the ocean currents system resulted in the reduction of gene exchange from north to south during the spawning period and expanded the genetic divergence of M. meretrix between north and south samples. We believed that the results could provide genetic insights for fisheries management to plan the fisheries policy of M. meretrix and protect the natural resource.