Rare minnow (Gobiocypris rarus) is a Chinese specific small fish It has been widely used as an experimental animal in China for pollutant risk assessment for its small body size, continuous spawning, convenient maintenance and high sensitive to pollutants etc Cadmium is one of the most toxic heavy metals in the world, and the exposure caused damage of fish gills However, no data available to report the transcriptome alteration of gills in this fish by chronic cadmium treatment In order to better understand the biotoxicity mechanism of cadmium, and to find some other biomarkers, we here investigated the de novo transcriptome profile of rare minnow gills after 75 μg/L waterborne CdCl2 exposure, by Illumina sequencing And data showed that, genes encoding for cytochrome c oxidase subnnits, ribosomal proteins were highly expressed in gills After the waterborne cadmium exposure, a total of 452 genes were significantly altered with FDR<0 05 209 of which were upregulated Most of top 20 altered genes were involved in the immune system, which indicated the immune toxicity of cadmium Down regulation of TRIM, CF8A, GAPr, MHCII indicated declined antivirus and antibacterial ability after Cd exposure.Further qPCR analysis showed that, TRIM, CF8A and GAPr were significantly downregulated in both acute (no longer than 96 h by 2.0 mg/L cdamium) and chronic (35 days) waterborne cadmium treated gills, even by a trace dose (5 μg/L), thus these genes might be used as biomarkers for assessment of cadmium pollution.