The post larvae shrimp were first acclimated from salinity 25 to 55, and separately cultivated at the two salinities for 3 months. The growth performance of the shrimp was evaluated after the long-term high salinity cultivation. Then, we examined the transcriptome responses of gills and hepatopancreas from the shrimp with differential growth rates under the long-term high salinity stress using Illumina sequencing technology.