Internal viscera fish are potential sources of protein biomolecules of biopharmaceutical interest. However, this residue is frequently discarded inappropriately. The possibility to obtain by products of higher added value is a reality. Inside this view attention must be given to processes for the recovery and extraction of target molecules. However, the high cost of processing these residues is one of the obstacles to their reuse; techniques that facilitate their handling and make the process cheaper are desirable, such as extraction in a two-phase aqueous system. Thus, the aim of this study was to extract collagenolytic enzymes from common snook (Centropomus undecimalis) using a two-phase aqueous system (polyethylene glycol/citrate), according to the 24 factorial design, using as variables: molar mass of PEG (MPEG), PEG concentration (CPEG), citrate concentration (CCIT), pH, still, considering purification factor (FP), partition coefficient (K), and yield (Y). The collagenolytic activity of the crude extract was 102.41 U mg-1, after partitioning, was purified 3.91 times (MPEG: 8000; CPEG: 20.0%; CCIT: 20.0% and pH 6.0). Inhibition (U mg-1) was observed in benzamidine (22.51), TLCK (21.05), TPCK (21.29), and PMSF (23.05), signaling to be a serine-protease. The results showed the advantage of this semipurification technique as concerns to the low cost of extraction and purification, adding value to the fishing source material and allocating the residues from its processing to the industry.