Global concerns about environmental impact of leather industry have been forcing the tanneries to adopt cleaner leather processing technologies. Enzyme based leather processing methods have the potential to substantially reduce the pollution, toxicity and also improve leather quality. One such greener process option is the use of proteases in dehairing of skins and hides. But the important criterion in choosing enzymes for dehairing is the specificity towards the targeted biomolecules on skins. As the skin itself is a proteinous substance, use of non-specific proteases might degrade other skin proteins and cause damage to resultant leather. The present work deals with the comparative study on the specificity of a dehairing and non-dehairing protease isolated in our laboratory. Two proteases producing bacteria, Bacillus cereus VITSN04 and Bacillus megaterium VITSN02 were used in this study. Studies on the efficacy of enzymes to dehair goat skins revealed B.cereus protease exhibited potent dehairing efficacy whereas protease from B.megaterium did not. Dehairing and non-dehairing enzyme was identified as serine and metalloprotease respectively and optimal pH and temperature for activity were also determined. The activity of B.cereus enzyme to unhair was evaluated at its specificity level using protein substrates such as keratin, collagen and compared with B.megaterium protease. The results showed that the dehairing enzyme was non-keratinolytic and non collagenolytic. The SEM studies on the cross section of skin dehaired enzyme showed good fiber opening which could probably due to specific degradation of proteoglycanby the enzyme. This is yet to be confirmed using proteoglycan as substrate. The non dehairing protease had degraded keratin substrate but not collagen. This preliminarystudy signifies the importance of screening proteases for specificity before employing the enzyme for dehairing process.