Fragments of the mitochondrial gene (COI and 16S rRNA) and the nuclear marker (H3 and 28S rRNA) regions are suitable for phylogenetic relationship analysis. The phylogenetic relationships among nine S. diphos, S. olivacea, and ) collected from the coastal areas of China was analyzed through the sequencing of COI, H3, 16S rRNA, and 28S rRNA genes. The two mitochondrial genes, COI 16S rRNA, had an obvious AT-skewness, and their GC content were 41.17% and 41.01%, respectively, showing a certain degree of base preference. The overall transition/transversion bias of the four fragments (COI 5.073, 16S rRNA 3.042, H3 1.564, and 28S rRNA 1.480) were much higher than the critical value (0.4), which could offer effective phylogenetic information. As the genetic diversity parameters of all four markers in nine species had higher values (Pi<0.05, Hd<0.5) than most bivalve species, it is suggested that the species may have long history in the localities, and sufficient phylogenetic information. Among the nine species, the genetic average distances based on the COI gene were 0.087-0.331, and the genetic distances within species were 0-0.016. The minimum genetic distance was between , which was much higher than the average value (0.005) between most species of bivalves. The saturation of the nucleotide substitution process in the four markers was calculated as well. The third codon positions of the COI gene's transition and transversion substitutions reached the point of saturation, which means that the third codon positions of the COI gene could not provide effective information. The combined data set T12, including the four molecular markers without the third codon positions of COI, totaled 1555 bp in length. Phylogenetic trees constructed by the Maximum Likelihood (ML) and Bayesian Inference (BI) methods were consistent, and cluster analysis based on the data set T12 showed three separate lineages, corresponding to three morphologically defined subgenera:. Combining morphological and molecular evidence, the results support that has the closest phylogenetic relationship. The study sheds light on the genetic diversity and phylogenetic relationship of species occurring along the coast of China, which may be useful in genetic resource protection and sustainable use.