Abstract: In the present study, we compare the partial sequences of mitochondrial COI and 16S rRNA of five genus Mytilus to study their phylogenetic relationship. Using Perna viridis and Septifer virgatus as outgroups, phylogenetic trees are constructed based on neighbor-joining, maximum parsimony, maximum likelihood, Bayesian inference and combined Bayesian analyses methods. The result demonstrates that Mytilus edulis, M.galloprovincialis, M.trossulus, M.coruscus and M.californianus formed into two clades. Among the five Mytilus species, M.californianus is the most primitive, then comes M.coruscus. M.galloprovincialis and M.edulis show very close genetic relationship, and M.coruscus is closer to M.californianus than to M.edulis, M.galloprovincialis and M.trossulus. The molecular phylogenetic analysis provides theoretical reference for future comparative study on species evolution, immigration and breeding strategies of Mytilus.