This study aimed to evaluate the effect of squid protein hydrolysate prepared from protamex (P1, P2, P3) and alcalase (A1, A2, A3) enzymes respectively, at 0.5%, 1% and 1.5% concentration and also control sample (0%), on some physicochemical and organoleptic properties of low-fat set style yoghurt such as viscosity, synersis percentage, water holding capacity, acidity, pH, odor, taste, texture and color. Results showed that the lowest viscosity (416/66) was for control sample. Protein hydrolysates of both of enzymes increased viscosity while the highest amount was for P3 and A3. The highest pH and lowest acidity were for the control sample and protein hydrolysate in yogurt formulation decreased pH and increased acidity of samples. Maximum synersis obtained with control sample (4.47); protein hydrolysate decreased synersis while 1% protein hydrolysate with alcalase had the lowest synersis (0.33). Results of organoleptic tests showed that alcalase samples, especially in higher concentrations, modified odor and taste of low-fat yoghurt but these changes were not clear in texture and color. Generally, squid protein hydrolysate with alcalase and protamex in yoghurt formulation improved functional properties of low-fat yoghurt and it was more efficient in alcalase treatments in comparison with protamex.