This study was aimed to provide an alternative and eco-friendly method by using the alkaline protease (210.67 U/ml) in order to reduce the application of chemicals substance in leather manufacturing. Leather manufacturing creates environmental pollution regarded as a source of water pollution. In this research, alkaline protease was used specifically produced from Bacillus subtilis. The enzymes are used in the dehairing treatment of cowhides performed by single enzyme treatment and enzyme assisted treatment, meanwhile conventional treatment by using chemicals. The incubation time for dehairing of cowhides in single enzyme treatment within 24 hours under mild shaking condition at room temperature resulted in 60%-80% of hair removal and enzyme assisted treatment within 75% until 100% of hair removal. Meanwhile, the chemical treatment removed 100% under same condition within 2 hours. After dehairing treatment, scanning electron microscopy (SEM) is made to observe the grain surface of cowhides and histologic analysis to identify the epidermis and dermis layers. The grain surface of skin using enzyme treatment revealed by SEM was smoother and silkier than chemical treatment. Histologic analysis of the skin showed the quality of enzymatically dehaired was better compared with chemically treated one. The keratinized cell of the skin presence in enzymatically dehaired presence with non-collagenolytic activity in comparison with chemically treated skin. Keratinize cell represent the grain surface of leather determined the superiority good quality of leather. Collagen act as an important component of the hides. Based on the results, the application of enzyme assisted treatment in large scale dehairing skin trial is the alternative to reduce the application of chemicals.