The swimming crab, Portunus trituberculatus, is a commercially important fishery species and widely distributed on sandy and muddy bottoms in the coastal waters of Japan, Democeratic People’s Republic of Korea , China and Malaysia. It is a euryhaline crab species, surviving in wide-range salinity conditions, and water salinity condition influenced its artificial propagations significantly. Aquaporins (AQP) which belong to a major intrinsic proteins (MIP) family plays important roles in salinity stress response. In this study, aquaporins cDNA of Portunus trituberculatus was cloned by rapid amplification of cDNA ends (RACE) and named PtAQP. The full-length of PtAQP cDNA is 1 712 bp, including an open reading frame (ORF) of 771 bp which encodes a 256 amino acid polypeptide. Bioinformatics software analysis reavealed that PtAQP gene contains 6 transmembrane domains, 2 NPA structural units and conservative amino acid sequence which is matched to MIP family. Homologous analysis showed that PtAQP of Portunus trituberculatus has the highest homology to AQP1 of Callinectes sapidus. The quantitative real-time RT-PCR showed that PtAQP gene could be detected in all tested tissues of Portunus trituberculatus, with the highest expression level in stomach. After challenged by high and low salinity, the expression of PtAQP gene in gill and hepatopancreas of Portunus trituberculatus first fell then rase. Our results confirmed the osmotic regulation function of PtAQP gene and revealed the regulatory mechanism of PtAQP gene under salinity stress.