Abstract: Based on about 400 bp sequences, nucleotide sequences of Cytochrome (Cyt b) segments of mtDNA wereanalyzed for anadromous Coilia ectenes, freshwater resident C. ectenes and C. mystus in the Yangtze River, China, todevelop a reference data for larval species identification of genus Coilia. The genetic distance ranged from 0 to 0.5%between the anadromous and freshwater resident C. ectenes, 7.9% to 8.9% between C. mystus and the anadromous C.ectenes, and 7.7% to 8.6% between C. mystus and the freshwater resident C. ectenes. Neighbor-joining (NJ) moleculardendrogram using Kimura 2-parameter based on the sequences of Cyt b gene showed individuals of the anadromous andfreshwater resident C. ectenes mixed into a cluster, and those of C. mystus forming another cluster. Thus, larvae of C.mystus could be distinguished from that of C. ectenes through Cyt b analysis. Nucleotide sequences of Cyt b of larvae ofgenus Coilia collected from the Yangtze Estuary were analyzed, and compared to the reference established above. Geneticdistance ranged from 0.1% to 0.5% between the larvae and the anadromous and freshwater resident C. ectenes, and8.3% to 8.8% between the larvae and C. mystus. NJ molecular dendrogram showed that all the larvae and the anadromousand freshwater resident C. ectenes clustered together, while individuals of C. mystus forming a separate cluster.Thus, the larvae were not of C. mystus. As there is no freshwater resident C. ectenes inhabiting in the Estuary, the larvaeshould be of the anadromous C. ectenes.