In order to explore the relationship between salinity effects and transcriptome of (Coilia nasus) gill tissues, transcriptome sequencing and analysis were performed on the gill tissues of Coilia nasus from waters with different salinity in the Dayang River basin. The results showed that 70964 unigenes were annotated. The unigene sequence of Coilia nasus was closest to that of Atlantic Herring (Clupea harengus). The proportion of unigenes related to cell process, biological regulation and metabolic process was high. Transcriptome expression related to metabolic function was very vigorous in the gill tissue. Organismal Systems and Environmental Information Processing have the largest number of unigene.