Microorganisms can spread on the surface of banknotes and cause many infectious diseases. Chitosan nanofibers (CNFs) and cellulose nanocrystals (CNCs) are nanomaterials, which can affect the antimicrobial properties. In this study, the fungal species that grew on the surfaces of collected banknotes from different places were identified. To examine the antifungal effect of the both nanomaterials on the banknotes, the stable coatings using CNFs and CNCs emulsions were prepared by roller coating. The results revealed that the most colonies in the banknotes obtained from the bakeries and butcheries were Aspergillus sp., whereas the colonies in bus terminals and the hospitals were Aspergillus niger and Penicillium, respectively. The results showed that the CNCs had no antifungal effect alone on the aforementioned species, but it could improve the antifungal effect, adhesion, and stability of CNFs on the banknote surfaces. This study suggested a new approach to decrease the infection spreads through banknotes.