Amylase has a lower activity in carnivorous fish species, particularly in Atlantic salmon. We report the first cloning of a salmonid alpha-amylase cDNA from Atlantic salmon, a major species in aquaculture. By amino acid alignment of several species, we identified a seven amino acid deletion in one of the large loops of the enzyme in relatively close proximity to the active site, that could impair substrate binding. We also found the signal peptide to be less hydrophobic compared to other species. This may affect import into ER during protein synthesis. Active site residues were shown to be conserved. Amylase mRNA expression was shown in pancreatic tissue, liver, and in the heart. Using blocked p-nitrophenyl-maltoheptaoside as a substrate, we measured a low amylase activity in Atlantic salmon intestinal content, which was about half of the activity measured in Atlantic cod, whereas activity measured in rainbow trout was fourteen times higher. Amylase activities in all three species showed similar degree of reduction in hydrolytic activity in a dose-response trial with a wheat amylase inhibitor preparation. This indicates similar specific activity per amylase molecule.