46 Pyrus germplasm accessions were inoculated with the fungal block(Valsa mali var.pyri) on the excised twigs for two years,and the relative POD,SOD activities,total phenolic content and tissue looseness were measured.The contents of SA and JA were determined by using ELISA.According to SA and JA synthesis related genes(PAL,ICS,AOS and AOC) fragment sequence,which were obtained from RNA-Seq,the relative expression levels were analyzed by real-time quantitative PCR (qRT-PCR) technology.The results showed that:(1)Differences in disease incidence and severity were found among germplasm accessions.In general,the cultivars of P.ussuriensis Maxim.are canker resistant,whereas most varieties of P.communis L.are canker sensitive.(2)There was no significant correlation between POD,SOD activities and tissue looseness,related positive correlation between total phenolic content in phloem of twigs.(3)For ‘Qiubai’,the endogenous SA and JA levels were increased after applied with V.mali var.pyri.The expression levels of PAL and AOS also increased under the treatment of the pathogen.However,the contents of SA and JA were no significant changed to the pathogen in ‘Chili’.Consistent results were found in the expression of PAL,ICS,AOS and AOC genes.Analysis showed that disease severity was positively correlated with total phenolic content.SA and JA may participate in the response of pear to the pathogen of V.mali var.pyri.