A total of 82 fungal isolates was obtained from wheat kernel samples affected by fusarium head blight collected from 20 locations in southern Brazil. Polymerase chain reaction (PCR) assays were used to characterize trichothecene mycotoxin genotypes [deoxynivalenol (DON), nivalenol (NIV) and two acetylated derivatives of DON]. To identify isolates that producing DON and NIV, portions of the Tri13 gene were amplified. To identify 3-acetyl-deoxynivalenol (3-ADON) and 15-acetyl-deoxynivalenol (15-ADON) genotypes, portions of Tri3 and Tri12 were amplified. Nearly all of the isolates studied (76/82) were of the DON/15-ADON genotype. Six of the isolates were of the NIV genotype. The DON/3-ADON genotype was not observed. Portions of three genes were sequenced from representative isolates of the NIV and DON/15-ADON genotypes and compared with sequences from curated reference isolates of Fusarium in GenBank. blast queries for individual gene sequences and pairwise comparisons of percentage identity and percentage divergence based on 1676 bp of concatenated DNA sequence suggested that the isolates representing the DON/15-ADON genotype were Fusarium graminearum sensu stricto and the isolates representing the NIV genotype were Fusarium meridionale. This is the first detailed report of trichothecene mycotoxin genotypes of F. graminearum and F. meridionale in Brazil.