Conventional chitosan synthesis via chemical route is polluting and results poor quality chitosan. Here, autochthonous fermentation of prawn shell waste was carried out as an alternative to existing chemical and biological synthesis methods. Prawn shell waste was incubated in sugarcane molasses at 10% (w/v) as carbon source and different concentration of salt; 2.5, 5.0 and 7.5% (w/v) in an airtight fermenter for 14 days. The physicochemical characterization of autochthonously fermented chitosan (AFC) were analysed by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and elemental analyser (EA). The degree of deacetylation (DD%) of AFC with 5% (w/v) salt concentration was the highest among other AFC with different salt conditions and control setups at 73.9%, while XRD showed degree of crystallinity of 96.81% and EA showed carbon/nitrogen ratio of 7.28%. By comparison, commercial chitosan had degree of deacetylation (DD%) of 78.47%, carbon/nitrogen ratio of 6.49% and degree of crystallinity of 84.54%. In conclusion, physicochemical characteristics of AFCs were comparable to commercial chitosan.