Fusarium graminearum and F. culmorum are phytopathogenic species that cause head blight and crown rot diseases in cereals worldwide. These two phytopathogenic fungi show great variation in terms of phenotypic, biochemical and genetic characteristics. In this study, linear growth rate, thiophanate methyl (TPM) resistance, survival and toxin production- associated gene expressions, and beta-tubulin nucleotide sequence knowledge of F. graminearum from Turkey and Iran and F. culmorum isolates from Turkey were investigated. The mean linear growth rate values of isolates ranged from 7.58 to 15.16 mm/day. In TPM resistance analysis, each isolate was characterized as highly sensitive to TPM, with IC₅₀ values between 2 and 4 μg/ml TPM. TPM-subjected isolates showed decreased tri5 gene expression and increased Mgv and StuA expression. Amino acid conservations at codons 198 and 200 in the beta tubulin gene were also investigated in order to confirm TPM resistance and reveal genetic diversity in Fusarium species. Each isolate showed conserved amino acids at 198 and 200 codons, resulting in sensitive genotypes. The bootstrap support value for genetic similarity was more than 70%. Findings obtained from this study showed that Fusarium isolates that cause head blight and crown rot in Turkey have a low level of variation in terms of phenotype and genetic characteristics. Moreover, this is the first report to show that TPM led to a potential decrease in toxin production-associated genes and increased potential of sexual/asexual reproduction genes. Results could provide improved and comprehensive data for the struggle against Fusarium pathogens.