black stem is one of the most important fungal diseases of sunflower caused by Phoma macdonaldii. In this study, expression level of some transcription factors (TF) including HD-Zip, AP2 domain, MYB- related, WRKY family and MYB family were studied using quantitative RT-PCR in sunflower genotypes, including ENSAT-B5 (susceptible to all 3 studied isolates; MA6, MP8, MP10), AS613 (resistant against MP8 and MP10 and susceptible to MA6), and M5-54-1 (a mutant genotype, resistant against MA6 and MP10 and susceptible to MP8) following infection by MA6, MP8 and MP10 isolates of P. macdonaldii. Among studied TFs, the expression level of two TFs, HD-Zip and MYB-related, were significantly different in genotype-isolate combinations but the expression level of three other TFs including AP2 domain, WRKY family and MYB family, were not significantly different in several genotype-isolate combinations. The expression of HD-Zip and MYB-related were suppressed in infected genotypes. Results revealed that increased repression of HD-Zip and decreased repression of MYB-related are affective in induction of resistance to MP8 and MP10 isolates in AS613 genotype. In this study, the induction of resistance in mutant genotype against MA6 and MP10 isolates was accompanied with decreased suppression of HD-Zip and MYB-related genes.