The Na+/K+-ATPase (NKA) is considered as the main pump involved in active ion transport. In the European sea bass, Dicentrarchus labrax, we found two genes encoding for the alpha 1 subunit isoforms (NKA α1a and NKA α1b). NKA α1a and NKA α1b isoform amino acid (aa) sequences were compared through phylogeny and regarding key functional motifs between salmonids and other acanthomorph species. Analysis of aa sequences of both isoforms revealed a high degree of conservation across teleosts. The expression pattern of both nka α1a and nka α1b was measured in the gill, kidney and posterior intestine of fish in seawater (SW) and transferred to fresh water (FW) at different exposure times. Nka α1a was more expressed than nka α1b whatever the condition and the tissue analyzed. After long-term salinity acclimation (2.5 years) either in FW or SW, transcript levels of nka α1a were higher in the kidney followed by the posterior intestine and the gill. Compared to SW conditions, expression of nka α1a in FW was significantly increased or decreased, respectively, in gill and posterior intestine. In contrast, branchial nka α1b was significantly decreased in FW-acclimated fish. Short-term FW acclimation seems to rapidly increase nka α1a transcript levels in the kidney unlike in gill tissues where different gene expression levels are detected only after long-term acclimation.