Abstract This work aimed to characterize acid and alkaline proteases extracted from farmed giant catfish ( Pangasianodon gigas ) viscera by using the aqueous two-phase system (ATPS). Determinations of optimum pH and pH stability, optimum temperature and thermal stability, salt stability and hydrolysis activities against bovine muscle protein and gelatin were performed. ATPS consisting of 20% polyethylene glycol (PEG1500)–15% MgSO 4 or 15% PEG2000–15% NH 3 C 6 H 5 O 7 was used for acid and alkaline proteases extraction. The optimum pH and temperature for acid protease was 3.0 and 40 °C, while alkaline protease was 9.0 and 60 °C. High pH stability of the enzymes was found in the ranges of 1.0–5.0 and 8.0–12.0 for acid and alkaline proteases, respectively. About 40 and 60% activities reduction of acid and alkaline proteases were observed when incubated at 90 °C for 30 min. In addition, 0.5% NaCl addition decreased >50% of total enzyme activities. Hydrolytic activities of the acid and alkaline proteases against bovine muscle protein and gelatin were in the concentration dependent manner as clearly indicated by SDS-PAGE. The results showed that the acid and alkaline proteases obtained from farmed giant catfish viscera could be useful for food protein hydrolysate production.