The current disposal of fish processing waste is causing environmental problems that have become an issue of public concern. Fish waste could be utilized for production of animal feed, biodiesel, natural pigments, food products and pharmaceuticals.Major attention was also directed to the recovery of valuable biomolecules such as collagen ω,-3 fatty acid, trypsin, chymotrypsin and elastase. Among these molecules, pepsin is one of the most beneficial and useful biomolecule that can be recovered from fish wastes.Pepsin is important aspartic proteases with many unique characteristics. It has several industrial applications including collagen extraction, cheese making, fish silage making, fish processing as well as use in medical research. Fish pepsin is primarily present in fish stomach and has a characteristic pH optimum of 2.0-4.0, distinct pH stability ≤ 6.0, a distinct optimum temperature of 30-55ºC and specific thermal stability ≤ 40-50ºC. Pepstatin A can strongly inhibit the pepsin activity while PMSF, E-64 and EDTA have a negligible impact. SDS, cysteine and aliphatic alcohols, have been identified as effective inhibitors while ATP, molybdate, NaCl, MgCl 2 , and CaCl 2 do not inhibit the activity of pepsin. Pepsin is widely applied in collagen extraction, in digestibility therapy,as rennet substitute and. At present, conventional method and innovative method have been developed for fish pepsin recovery. In the conventional method (ammonium sulfate), the partition of pepsinogen (PG) is mainly based on (a) crude enzyme extraction by homogenization and centrifugation, (b) purification of PG by gel filtration and anion exchange chromatography and (c) activation of PG under the acidic condition. The innovative recovery is based on aqueous two-phase system (ATPS). The conventional method is used for high purification while the ATPS is used for partial purification. Enzyme activity and concentration, specific activity (SA), purification factor (PF), molecular weight, and homogeneity, isoelectric point (pI) and are used to assay fish pepsin.