The inhibition of chitosan on Alternaria alternata in vitro was initially investigated. Spore germination, the radial growth and morphological changes of the hyphae of A. alternata was observed. Results showed that 6.0 mg/mL chitosan inhibited spore germination of A. alternata by 79.54%; inhibited the radial growth by 85.89%. Chitosan of different concentrations induced morphological changes of the hyphae, and when the concentration reached to 3.0 mg/mL, the hyphal morphology began to change. And the hyphae changed from long and thin to bead-like, and also partly swelled.