Abstract: Bioinformatics methods were used to detect and analyze chitinase genes from the genome of Pestalotiopsis kenyana PG52. The chitinase genes related to mycoparasitism were screened by detecting the expression of genes induced by aecidiospores at different time periods. Results showed the PG52 harbors 20 GH18 family chitinase genes and a GH19 family gene with molecular weights of 38.0–177.2 kDa and theoretical pI of 3.97–9.25, 7 genes had signal peptides and 13 genes were located in extracellular. PGChns gene contained the conserved domains of the GH18 family or the GH19 family. Additionally clustering analysis with Trichoderma spp. showed that PGChns of GH18 family can be classified to 7 sgA, 4 sgB, 8 sgC, and 1 sgD chitinase genes. After rust spore induction, 18 genes were differentially expressed, 7 genes were most highly expressed at 24h induction, 6 continuously down-regulated genes after induction, 4 genes with most high expression after 72h induction. Subsequently, 6 genes with high expression or great fold change were selected for RT-qPCR, and the results suggested the highest expression level of differently expressed genes was observed after 72h induction. The up-regulated expression of PGChns after induction is likely to play a role in destroying the rust spore wall during the reparasitization of PG52 strain, while the mechanism of its reparasitization action is not yet clear.