Collagenase existed in the internal organs of filefish Novoden modestrus was isolated with ammonium sulfate and was purified by ion exchange column chromatography with DEAE-Sephadex A-50 and gel filtration with Sephadex G-150. The activity of the purified enzyme was increased 92.4 folds than that of the crude one and the yield of the purified one was $10.9\%$. The optimum conditions showing the maximum activity of the crude enzyme to digest insoluble collagen(Type I) were $55^{circ}C$ and pH 8.0, while those showing the maximum activity of the purified one were $55^{circ}C$ and pH 7.75. However, the use of the crude enzyme for skinning of filefish was more profitable because the yield was 800 folds higher than that of the purified one and the cost was also able to economy. When hydrolysis for skinning of filefish was conducted with $0.3\%$(w/w) crude collagenase at $50^{circ}C$ and pH 8.0 for 3hrs, there was some problem to cause a damage on muscle of the fish by heat. To solve such problem for the skinning, the hydrolysis at $18^{circ}C$ for 4hrs with $0.3\%$ (w/w) crude enzyme after pretreated with 0.5M acetic acid for 10 min provided a good result for skinning of filefish.