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.