Here we used morphological discrimination analysis and RAPD analysis to study the phylogenetic relationship and genetic diversity of three populations of Tegillarca granosa in Yueqing Bay Wenzhou area.The results showed as follows: (1) The phylogenetic relationship of Yueqing population and Korea population is closer than that of Yueqing population and Fujian population on molecular level, although the geography relationship of Yueqing population and Fujian population is much closer.A possible explanation is that the gene pool of Yueqing population was contaminated by Korea population.(2) However,the phylogenetic relationships of three populations,which are based on morphology data,consisted with the geography relationships.It shows that the degree of contamination of Korea population is not enough to change evidently the shell outline of Yueqing population.(3) From highest to lowest,the genetic diversity of three populations is Korea,Yueqing,and Fujian.Their average heterozygosity is(0.275 4),(0.257 5) and (0.247 3),and the average genetic distance of each population is 0.304 8,0.240 1 and 0.211 5,respectively.These also show that the genetic diversities of the three populations maintained high level.(4) There 4 specific bands appeared in Yueqing population using random primers S.418,(S.359) and S.431 PCR amplification,and they could be used as molecular markers of Yueqing population.