Three Liza species exhibiting a dorsal keel have been identified based on morphology: Liza affinis, Liza carinata, and Liza klunzingeri. To confirm the validity of the species by molecular methods, we sequenced a fragment of the cytochrome oxidase subunit I (COI) gene of mitochondrial DNA of Liza affinis and Liza klunzingeri from coastal waters of China and Pakistan, respectively. Sequences of L. carinata were obtained from GenBank. A neighbor-joining tree showed the specimens to form a strong monophyletic group. The mean within-species genetic distances for L. affinis, L. carinata, and L. klunzingeri were 0.26%, 0.52%, and 0.47%, respectively. The mean genetic distances among L. affinis, L. carinata, and L. klunzingeri ranged from 12.22% to 14.74%, higher than the threshold for species delimitation. The results confirmed the taxonomic validity of the three Liza species and verified that the COI gene could provide effective DNA barcoding for identification.