The role of Fusarium graminearum trichothecene-chemotypes in disease outcomes was evaluated by point inoculation in a series of wheat lines with different levels of resistance to Fusarium head blight (FHB). Four inocula, each consisting of a composite of four strains with either 15-acetyldeoxynivalenol (ADON) chemotypes from “traditional” or emergent populations, a 3-ADON chemotype, or a nivalenol (NIV) chemotype, were compared. The evaluated wheat included Canadian lines with different levels of FHB resistance/susceptibility and double haploid lines developed from crosses of these lines. Highly resistant lines were resistant to infection by all of the F. graminearum chemotypes evaluated. In the moderately susceptible/resistant wheat lines, the 3-ADON producers and the emergent 15-ADON population were, in some instances, more aggressive and resulted in higher Fusarium damaged kernel scores and levels of trichothecene accumulation. The data presented in this study demonstrate the importance of growing highly resistant wheat cultivars in the current climate of an evolving F. graminearum population, and suggest that moderate levels of FHB resistance may not be sufficient to minimize trichothecene contamination of grain from F. graminearum–infected wheat.