All plants and pathogens inevitably produce reactive oxygen species (ROS) during the "attack and defense" process. The fungal antioxidant system to host-generated ROS is critical for pathogenesis during plant-pathogen interaction. In the present work, we generated A. alternata Yap1 disrupted mutant, which showed an increased sensitivity to oxidative stress and decreased virulence on Citrus leaves. The gene expression pattern of Alternaria alternata wildtype and Yap1 under vegetative growth, and ROS stress and plant-pathogen interaction were compared to elucidate the transcription network. In addition, comparative transcriptome analysis of oxidant-sensitive mutants Glr1, Tsa1, Trr1 were performed to identify the genes and pathways related to ROS tolerance. Gene Ontology (GO) analysis showed that many genes related to the oxidation-reduction process are differentially expressed in Yap1 mutant as well as the wildtype under oxidative stress and plant-pathogen interaction, further confirming that the important role of Yap1 in ROS tolerance and pathogenicity. KEGG enrichment analysis revealed that many critical metabolic pathways are significantly affected after the disruption of the Yap1 gene or inoculation with hydrogen peroxide or Citrus leaves. Taken together, our study underlines the essential role of antioxidant systems regulated by stress-responsive transcription regulator Yap1 contribute to ROS stress resistance that is critical to pathogenesis during plant-pathogen interaction in A. alternata.