The fatty acid status of the total lipids was studied in smolts of the brown trout and the Atlantic salmon collected in summer in the Indera River (White Sea basin). Higher 18:3ω-3/18:2ω-6, ω-3/ω-6, and 20:4ω-6/18:2ω-6 ratios were found in smolts of the Atlantic salmon in comparison to smolts of the brown trout. A higher amount of essential fatty acid 18:2ω-6 and an increased ratio of the sum of polyunsaturated fatty acids to the sum of saturated fatty acids in smolts of brown trout were observed. We have registered the differences in the ratios of the fatty acids, including physiologically active ones, which indicated species-specific physiological and biochemical processes during smoltification.