Six species of genus Anguilla, including Anguilla rostrata, A. anguilla, A. bicolor pacifica, A.marmorata, A. australis and A.japonica are cultured in China. Misidentification on the fry will impact farmers’ income because of different Anguilla species with different prices in China. In this study, we tried to use two molecular markers (1179bp length mitochondrial COⅠ gene and 633bp length COⅡ gene) to discriminate the six species based on 54 fry individuals. The percentage of variable sites in COⅠ and COⅡwas 17.98% and 16.45% respectively. And the percentage of parsimony informative sites was 12.16% and 10.11% in COⅠ and COⅡ. The negative bias for G was observed in both COⅠ and COⅡ genes in checked samples, and their G frequences were 18.45% and 16.67% respectively. The pairwise distances based on either COⅠor COⅡ among six eel species were almost more than 2% except for only one between A. rostrata and A. anguilla based on COⅡ, and the former was a little higher than the latter. But the genetic distances within each species were all less than 1% based on two genes. Although there existed a small difference between two cluster results of six eel species,which was based on COⅠ gene or COⅡ gene, all individuals of each species formed a strong monophyletic group on NJ and Mrbayes trees. Taken together, both COⅠand COⅡgenes are good molecular markers to be used in species identification in genus Anguilla, and our results may be helpful for eel aquaculture industry in China.