In this study, the transcriptome of a prochloraz-resistant strain HSYN1 and a prochloraz-susceptible strain HSHN1 had been sequenced and analyzed. The purpose of this work was to identify the differences in the transcription profiles between prochloraz resistance and susceptibility strain, and to identify the key DEGs involved and their related functions. These results will lay the foundation for elucidating the molecular mechanisms underlying resistant to prochloraz, and make a meaningful contribution to prevent and cure the P. italicum.