Abstract: We used PCR to amplify the complete sequences of mitochondrial DNA (mtDNA) control region of 2 Trachurus japonicus from South China Sea, and then aligned them by Clustal X with 8 other species of the genus Trachurus from GenBank. According to the alignment and structure comparison, the mtDNA control region of the genus Trachurus can be divided into 3 domains: termination associated sequence domain (TAS), central conserved domain (CD) and conserved sequence block domain (CSB). We identified 2 termination-associated sequences (TAS) and 3 conserved blocks (CSB-F, CSB-E and CSB-D) in CD domain as well as 3 conserved sequence blocks (CSB-1, CSB-2 and CSB-3) in CSB domain. Taking Siniperca chuatsi as outgroup, the molecular phylogenetic relationship among 9 Carangidae was analyzed using neighbor-joining (NJ) method and maximum parsimony method in MEGA 4.0. Results show that the genus Trachurus fishes belong to a monophyletic group: T.picturatus, T.murphyi, T.symmetricus, T.capensis and T.trachurus gather into one cluster; T.mediterraneus, T.declivis, T.japonicus and T. novaezelandiae gather another. T.japonicus does not form into an independent group but is merged into T.declivis and T.novaezelandiae. Thus, it is suggested that T.japonicus and T.novaezelandiae may be 2 synonyms.