Abstract: Accurate species identification is crucial for eel aquaculture, especially when increasing taxa of the fish were raised in the eel farms in China. This study applied a pair of specific primers from the conservative fragment of mtDNA COI gene in Anguilla to amplify 109 DNA samples extracted from 21 batches of eel juveniles for taxon identification. It was found that a specific 652bp fragment could be amplified from all of the samples. The BOLD Identification System (Barcoding of Life Data Systems: www.boldsystems.org) was used for sequence similarity search on the COI genes. Seven species, including A. japonica, A. rostrata, A.anguilla, A.marmorata, A.mossambica, A.luzonensis and A.bicolor pacifica, were identified. The cluster analysis showed 7 main clades with high rate of support at the nodes. It suggested that the COI identification method could be satisfactorily employed for eel juveniles identification. Incidentally, during the course of this study a former mistaken identification on a batch of juvenile fish was discovered. Therefore, the DNA barcode-based identification method was highly recommended for implementation to benefit the commercial trade and eel aquaculture.