Estuarine tapertail anchovy (Coilia nasus) is a commercially important species. However, eco-environment deterioration and overfishing have almost caused extinction of the species in the Yangtze River. Therefore, it is very urgent to perform genetic research on C. nasus to protect the wild population. In this study, we sequenced the brain transcriptome of C. nasus using Illumina Hiseq 4000 platform. We obtained 123,764 unigenes with an average length of 1092 bp and a total of 115,169 putative Simple Sequence Repeats (SSRs). Among them, 37 SSRs were selected for the validation experiments. All of the loci were found to be polymorphic and showed bi-allelic in 60 individuals of C. nasus. These SSR markers should not only be useful for population conservation, but also for construction of genetic linkage map and economic performance improvement of C. nasus.