The classification and evolutionary relationship of Carangidae has remained much controversy between conventional morphological studies and molecular phylogenetic studies. In this study, the 16S ribosomal RNA gene of 9 species of 8 genera from Carangidae in China sea were amplified using PCR technique. Approximately, 598 bp gene fragments were obtained. The resulting data were combined with Pomadasys maculates designed outgroup and additional homologous sequences of 3 species from Carangidae downloaded from GenBank to form the analysis matrix. Nucleotide composition frequencies, Kimura-2 parameter genetic distance and transition/transversion ratios were analyzed with the MEGA 3.0 software. Molecular phylogenetic trees were constructed by maximum parsimony (MP) and neighbor-joining (NJ) methods. The results were as follows: (1)There were insertions and deletions of base pairs in the aligned base pairs. 146 bp variable site were 2.17, suggesting that the sequences had not reached saturation. The average percentage divergence was 8.22%; (2) Fish classification system of Carangidae classified four subfamilies as Caranginae, Seriolinae, Trachinotinae, Chorineminae was acceptable, according to the partial sequence of mitochondrial 16S ribosomal RNA gene; (3) It’s improper to define subgenus in Caranx of Caranginae; (4) Alepes djedaba and Alepes kleinii had a close relationship, should be belong to the same Alepes genus, as the difference of partial 16S ribosomal RNA gene between them was only 1.07%.