We compared our transcriptome data with Portunus trituberculatus EST sequences obtained from NCBI and showed that more than half of the EST sequences can be matched in the transcriptome data, whereas only 2.05% of the transcriptome unigene sequences can be found in the ESTs library. It suggests the transcriptome data Chloroquine Phosphate provide abundant information besides the now available ESTs sequences. After a homology search in the non-redundant protein D-Pantothenic acid sodium database at NCBI, a total of 13,212 unigenes, which took up a proportion of 13.98% in all the unigenes, showed significant BlastX hits of known protein sequences. The distribution of significant BlastX hits over different organisms was also analyzed. Due to the lack of genomic information in Portunus trituberculatus, the majority of the assembled sequences matched genes from microcrustacean arthropod Daphnia pulex which have full genomic information. Comparison of gene expression among the different treatment groups in the current experiment is helpful for identification of candidate genes underlying response to salinity stress in Portunus trituberculatus. In this study, we detected a total of 1,705 unigenes were differentially expressed between the comparison of LC vs NC and HC vs NC |>1), which significantly more abundant than the data of previous study, in which only 417 differentially expressed genes were found after two different salt challenges via cDNA microarray technology. The results prove that the next generation sequencing methods should be more powerful than cDNA microarray technology in expression analysis because it can provide high data output and recognize new unigenes or unique isoforms present in transcriptome. Many fewer differentially expressed unigenes were found in the LC Vs. NC compared with that of HC Vs. NC. To further unravel the significantly altered biological processes upon salinity stress, the up- and down-regulated genes categorized into eight patterns based on expression profiles were subjected to the GO term enrichment analysis. The results revealed that a total of 454 unigenes were enrichmented in 63 processes, among which, the differentially expressed unigenes in low salinity stress were enrichmented in 25 processes. The differentially expressed unigenes in high salinity stress were enrichmented in 58 processes. Further analysis found, 5 and 38 processes were only enrichmented in low salinity stress or high salinity stress respectively, another 20 processes were enrichmented in both stress. In conclusion, our analysis uncovered: 1, more genes and processes were involved in high salinity stress adaptation than low salinity stress adaptation. 2, the processed involved in low salinity stress were mainly supressed, and the processed involved in high salinity stress were mainly induced. 3, hypoosmoregulation and hyper-osmoregulation mechanisms share some processes but also has many differences. Past research has revealed two major strategies, i.e. the ��limiting process�� and the ��compensatory process��, that are adopted by crustaceans for osmoregulation and both are predominately accomplished by the gills. A ��limiting process��is a strategy whereby the maintenance of hemolymph osmolality/ions is accomplished by adjusting the permeability of the boundary structures, which can be a highly effective method to reduce ion diffusion and water inux rather than solely relying on the more energetically demanding mechanisms of ion transport. It has been suggested that the mechanisms during long term salinity exposure is often the result of gill membrane fatty acid compositional changes. In the case, generally membranes containing higher proportions of fatty acids with high unsaturation indexes.