Chitosan is natural polymer with abundant availability and unique characteristics. The purpose of this study was to investigate the effects of various isolation methods on chitosan properties. Chitosan was obtained by isolation method using oyster pearl shell (Pinctada maxima sp.). The parameters of the deacetylation process are the comparison of heating method with microwave method and the comparison of microwave power. Chitosan was characterized for degree of deacetylation (DD) and functional groups by FTIR, and viscosity by Brookfield viscometer. The microwave method was faster than the heating method. Then, the larger mass of shell and %NaOH produced a higher DD of 89.75%. However, the use of 60g mass and 60% NaOH resulted in an already high DD of 81.96%. Furthermore, variation microwave power showed the highest DD at high power. FTIR spectrum analysis showed the appearance of chitosan functional groups, OH and NH2 groups. The viscosity value decreased as the microwave power increased. Based on this study, different isolation methods affect the quality of chitosan. However, it’s necessary to conduct more detailed research related to changes in chemical structure. Therefore, oyster shells can produce chitosan as a source of natural polymers with different characteristics.