The results of experimental studies on changes in lysosomal protease activity in muscles of Atlantic salmon on the early stages of ontogeny are presented in the article. The main lysosomal proteolytic enzymes (cathepsins B and D) participated in lysosomal autophagic cell system and varied in chemical composition, catalysis, pH optimum, substrate specificity, with respect to ingibitors, functional activity were investigated. A relatively high activity of the main lysosomal aspartate type endoproteinase (cathepsin D) on the early stage of young’s-of-the-year salmon (0+) was shown. It indicates the leading role of the enzyme in complete protein degradation required to supply with amino acids and peptides to maintain immediately the homeostasis in juveniles. The activity of lysosomal cystein type proteinase (cathepsin B) increases as the development of salmon progresses from the stage 0+ (fingerlings) to stage 2+ (parr). It shows the intensification of proteolysis due to increase of growth rate. Multidirectional change in the activity of the main lysosomal proteases (increase in the activity of cathepsin B and decrease in the activity of cathepsin D) in the muscles of Atlantic salmon of ages 0+, 1+, 2+ indicates the stage-specific character of the involvement of hydrolases studied in intracellular proteolysis of juvenile salmon.