Protein quality of protein hydrolysates prepared from dark flesh skipjack tuna, hydrolyzed using 2.04 % Alcalase® (FPH-A) and 3 % Protamex® (FPH-P) were evaluated and compared with commercial fish protein hydrolysate (FPH-C). The protein quality was determined using the analysis of molecular weight, amino acid profile, amino acid score/chemical score, protein digestibility correction amino acid score, essential amino acid index, protein efficiency ratio, biological value and its in-vitro digestibility. The results conclude that the FPH-C possessed wider distribution of molecular weight ranged from 237 Da to 11770 Da (mean 3231), in which the largest proportion were at <1000 Da (20%) and >5000 Da (20%). FPH-P possessed narrower distribution range (1210-7246 Da) which 50% of the protein was at 2000-3000 Da. On the other hand, FPH-A's was at range of 730-6440 Da dominated with low molecular weight protein (40% of 1000-2000 Da). Skipjack tuna hydrolysate prepared using Alcalase® showed higher aminoacids concentration, chemical score of protein, protein efficiency ratio (PER), biological value and protein digestibility correction amino acid score (PDCAAS) compared to hydrolysate repared using protamex and commercially sold hydrolysate tested.