We examined whether gene expression in the young salmon (Salmo salar) gill differs in relation to the salinity of their migration habitat by comparing three salmon stocks: (1) fish that migrate from a river system to Lake Saimaa, (2) fish that migrate to the brackish waters of the Baltic Sea, and (3) fish that migrate to the full-strength salinity of the Arctic Ocean. Transcripts of the gill tissue were measured at three successive developmental stages (parr, smolt and postsmolt) using the cDNA microarray in fish reared under common conditions. The changes in gene expression were qualitatively and quantitatively similar in the three stocks irrespective of the salinity of the natural growing habitat. This suggests that the parr—smolt transformation in the gill tissue of the landlocked fresh-water salmon stock is similar to the seawater migrating salmon. The transformation of the gill to a hypoosmotic organ in the freshwater salmon has been retained in evolution, possibly due to its adaptive role as a signal for migration from a relatively poor-growth environment of the river to a more productive lake habitat.