The dynamics of branchial Na+,K+,2Cl− cotransporter (NKCC) and Na+,K+-ATPase (NKA) expression were investigated in brown trout and Atlantic salmon during salinity shifts and the parr-smolt transformation, respectively. In the brown trout, Western blotting revealed that NKCC and NKA abundance increased gradually and in parallel (30- and ten-fold, respectively) after transfer to seawater (SW). The NKA hydrolytic activity increased ten-fold after SW-transfer. Following back-transfer to fresh water (FW), the levels of both proteins and NKA activity decreased. The NKCC immunostaining in the gill of SW-acclimated trout was strong, and mainly localized in large cells in the filament and around the bases of the lamellae. In FW-acclimated trout, immunostaining was less intense and more diffuse. Partial cDNAs of the secretory NKCC1 isoform were cloned and sequenced from both brown trout and Atlantic salmon gills. Two differently sized transcripts were detected by Northern blotting in the gill but not in other osmoregulatory tissues (kidney, pyloric caeca, intestine). The abundance in the gill of these transcripts and of the associated NKCC protein increased four- and 30-fold, respectively, during parr-smolt transformation. The abundance of NKA α-subunit protein also increased in the gill during parr-smolt transformation though to a lesser extent than enzymatic activity (2.5- and eight-fold, respectively). In separate series of in vitro experiments, cortisol directly stimulated the expression of NKCC mRNA in gill tissue of both salmonids. The study demonstrates the coordinated regulation of NKCC and NKA proteins in the gill during salinity shifts and parr-smolt transformation of salmonids. © 2002 Wiley-Liss, Inc.