To identify the species of the tapertail anchovies rapidly, Coilia brachygnathus, C. nasus and C. nasus taihuensis distributed in freshwater lakes of the Yangtze River Basin, single nucleotide polymorphism (SNP) molecular markers were developed to distinguish them. Twenty SNP markers were randomly selected with fixation index (F_st) of 1 from the 120 loci found between C. brachygnathus and C. nasus; and 10 SNP markers were ramdomly selected with high F_st value from the 21 loci found between C. nasus and C. nasus taihuensis for primers designing. Twenty C. brachygnathus, 20 C. nasus taihuensis and 12 C. nasus were randomly amplified and sequenced using the primers designed. The results showed that each of the 19 SNP markers can be used to completely distinguish C. brachygnathus and C. nasus, and no polymorphic sites were found in the other locus in the samples tested. Eight SNP makers were successfully amplified and used to distinguish C. nasus and C. nasus taihuensis. Marker Ct-Cn_wta showed the highest difference in genotype frequency between C. nasus and C. nasus taihuensis. When marker Ct-Cn_wtap and Ct-Cn_eif2b4 SNP were used, the successful identification rate on C. nasus and C. nasus taihuensis reached 100%. In conclusion, a robust and efficient method is provided to identify the tapertail anchovies, C. brachygnathus, C. nasus and C. nasus taihuensis using SNP molecular marker, which would provide an important tool for identification and conservation of the tapertail anchovies.