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. Taking 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.coruscus form into two clades. Among the five species of genus Mytilus, M.coruscus 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.coruscus than to M.edulis, M.galloprovincialis and M.trossulus. The molecular phylogeny analysis provides theoretical reference for future comparative study on species evolution, immigration and breeding strategies of Mytilus.