The basal transcription factor II H subunit tfb5 regulates gene expression and DNA repair. The roles of tfb5 in plant pathogenic fungi remain largely unknown. In this study, we investigate the function of tfb5 by knocking out tfb5ortholog (Aatfb5) in the phytopathogenic fungus Alternaria alternata. Aatfb5mutant decreases sporulation, slightly reduces growth on MM medium and significantly reduces virulence. Spores of Aatfb5 germinate at a rate similar to those of wild-type. Aatfb5 plays an important role in response to UV light, DNA-damage agents and oxidative compounds. Interestingly, Aatfb5 reduces pigments and biosynthesis of ACT toxin dramatically, indicating that Aatfb5plays a profound role in the production of secondary metabolites. In addition, deletion of Aatfb5 impacts cutinase activities. Taken together, Aatfb5 plays a critical role in DNA repair, pathogenicity and biosynthesis of secondary metabolites.