Abstract Na+/K+-ATPase is an important ion-transporting enzyme involved in osmoregulation. The swimming crab (Portunus trituberculatus) is a commercially important edible crab species in China. At salinities lower than 10 or higher than 40, its production is seriously impacted; however, the mechanisms of how the Na+/K+-ATPase of swimming crabs responds to salinity changes, is unclear. In the current study, the Na+/K+-ATPase α-subunit (NAKA) and β-subunit (NAKB) cDNA of P. trituberculatus was identified. Multiple alignment was performed and the expression of NAKA and NAKB in the 6th gills under different salinity conditions were detected using semi-quantitative RT-PCR. The results showed that NAKA and NAKB mRNA both increased significantly at day 1, but they were maintained at low levels when exposed to 40 salinity for a long time. The hematoxylin and eosin staining showed that ionocytes increased in size at 40 salinity, but decreased at 10 salinity. Immunocytochemical analysis revealed that NAKA signals increased with exposure to 40 salinity for one day, but the signals were not strong at 10 salinity. Comparison of the conserved NAKA domain of P. trituberculatus and the Chinese mitten crab (Eriocheir sinensis) showed that the polypeptide binding site (α-subunit/β-subunit interface) was different, which may be one of the reasons that P. trituberculatus is not as tolerant of fresh water as E. sinensis.