The study is an overview of the behavior of the wheat transcriptome to the Fusarium graminearum fungus using two different chemotypes. The transcriptome profiles of seven putative differentially expressed defense-related genes were identified by SSH and further examined using qPCR. Fusarium head blight (FHB) of wheat (Triticum aestivum L.), caused by several species of the fungus fusarium, is important in all wheat growing regions worldwide. The most dominant species in Canada is Fusarium graminearum (Fg). F. graminearum isolates producing mycotoxins such as 3-acetyl-deoxynivalenol (3ADON) and 15-acetyl-deoxynivalenol (15ADON). The objective of this study was to investigate the effect of the different chemotypes of Fg on the transcriptome pattern of expressed wheat genes. A cDNA library was constructed from infected "Sumai 3" spikes harvested at different times after inoculation with a macroconidia suspension. Employing suppression subtractive hybridization (SSH), the subtracted cDNA library was differentially screened by dot-blot hybridization. Thirty-one clones were identified; one was isolated and characterized, and transcriptome profiling of seven up-regulated putative defense-related genes was performed using quantitative real-time reverse-transcriptase PCR. These genes may be involved in the wheat-pathogen interactions revealing transcript accumulation differences between the non-diseased, 3ADON-, and 15ADON-infected plants. Additionally, significant differences in gene expression were observed between 3ADON- and 15ADON-infected plants which highlight the significance of a particular chemotype in FHB disease.