Silver carp (Hypophthalmichthys molitrix) skin (SCS) is available as low cost by-product in minced products manufacturing plants. Kilka fish (Clupeonella spp.) oil has a higher omega-3 fatty acids content compared to other Caspian Sea fish oils and higher nutritional value. In the present study, SCS was collected, hydrolyzed with alcalase, and its functional properties was investigated for the microcapsule stability of purified Kilka oil (PKO) at pH 6.8 and 3.4. Results showed significant changes of amino acids profiles during 6 h hydrolysis (p<0.05). Total hydrophobic amino acids decreased from 32.8% at 0.25 h to 24.9% after 6 h. Hydrolysates showed different radical scavengering activity during different hydrolysis periods. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavengering activity and Ferric reducing antioxidant power (FRAP) increased significantly during first hour, peaked at 4 h and then decreased slowly. Microemulsion was more stable at pH 6.8 compared with pH 3.4 and showed significant differences at 2-5 mg/mL of hydrolysate (p<0.05). As a general result, the use of hydrolysis of SCS and its antioxidant role in the production of stable emulsions containing PKO microcapsules is a valuable process for the enrichment of various kinds of foods.