Coilia ectenes, also called Coilia nasus, is an ecologically important species endemic to China. Due to habitat fragmentation, over-harvesting and water pollution, the natural germplasm of C. ectenes has declined dramatically in the recent decades. Thus, developing sufficient molecular markers for the conservation and molecular-aided selection of this species is urgent. In this study, 50 polymorphic single nucleotide polymorphism (SNP) markers were developed in C. ectenes based on the transcriptome database and characterized by genotyping 40 individuals using SNaPshot method. The minor allele frequency, the observed heterozygosity (H_O), expected heterozygosity (H_E) and polymorphism information content ranged from 0.1250 to 0.4875, 0.1750 to 0.7000, 0.2188 to 0.4997 and 0.1948 to 0.3744, respectively. Among these SNPs, sixteen loci were found to deviate significantly from the Hardy–Weinberg equilibrium after sequential Bonferroni correction (p < 0.05). These novel polymorphic SNPs will enable future genetics improvement of this species.