Enzyme based dehairing of animal skins in leather processing is considered a greener alternative to conventional chemical based dehairing process. The specificity based screening of proteases would be an important criterion as it would help in removing hairs by acting particularly on the proteoglycans holding the hair to the bulb without damaging the other proteins. The present paper describes a comparative study of the specificity of a dehairing protease with non-dehairing one isolated from Bacillus sps. Dehairing protease was found to be trypsin-like, non-collagenolytic and non-keratinolytic enzyme whereas non-dehairing one was a metalloprotease with non-collagenolytic activity but specificity for soluble keratin. Substrate specificity was studied using decorin as model proteoglycan. The dehairing enzyme was effective in digesting the core protein of the decorin as confirmed by high performance liquid chromatography analysis and SDS-polyacrylamide gel electrophoresis. The histochemical studies on dehaired skins also confirmed preservation of skin matrix with no visible damage to collagen. This study emphasizes the importance of screening proteases based on their specificity characteristics for effective and safer enzyme-only dehairing process. The acquired knowledge can be employed in formulating bacterial growth media to produce dehairing proteases that would help in commercial exploitation of this greener option.