We identified five Na+/K+-ATPase alpha-isoforms in rainbow trout and characterized their expression pattern in gills following seawater transfer. Three of these isoforms were closely related to other vertebrate alpha1 isoforms (designated alpha1a, alpha1b and alpha1c), one isoform was closely related to alpha2 isoforms (designated alpha2) and the fifth was closely related to alpha3 isoforms (designated alpha3). Na+/K+-ATPase alpha1c- and alpha3-isoforms were present in all tissues examined, while all others had tissue specific distributions. Four Na+/K+-ATPase alpha-isoforms were expressed in trout gills (alpha1a, alpha1b, alpha1c and alpha3). Na+/K+-ATPase alpha1c- and alpha3-isoforms were expressed at low levels in freshwater trout gills and their expression pattern did not change following transfer to 40% or 80% seawater. Na+/K+-ATPase alpha1a and alpha1b were differentially expressed following seawater transfer. Transfer from freshwater to 40% and 80% seawater decreased gill Na+/K+-ATPase alpha1a mRNA, while transfer from freshwater to 80% seawater caused a transient increase in Na+/K+-ATPase alpha1b mRNA. These changes in isoform distribution were accompanied by an increase in gill Na+/K+-ATPase enzyme activity by 10 days after transfer to 80% seawater, though no significant change occurred following transfer to 40% seawater. Isoform switching in trout gills following salinity transfer suggests that the Na+/K+-ATPase alpha1a- and alpha1b-isoforms play different roles in freshwater and seawater acclimation, and that assays of Na+/K+-ATPase enzyme activity may not provide a complete picture of the role of this protein in seawater transfer.