Root rot of pulse crops and Fusarium head blight (FHB) of cereals are important diseases that have significant negative impacts for Canadian farmers. Root rot is caused by a complex of pathogens, including Fusarium avenaceum (Fa) and Fusarium graminearum (Fg). In this project, we explored the role of mycotoxins, and other pathogenicity factors, in Fusarium root rot of pulses and studied the natural variation of Fa isolates from different host sources in their aggressiveness on peas, lentils and durum wheat. Forty-two isolates of Fusarium avenaceum collected from wheat, pea and lentil plants across from different regions in Canada were screened for aggressiveness on pea, lentil and durum wheat. A general trend of higher aggressiveness was identified in the pea isolates compared to those of wheat. Baseline secondary metabolite profiles were established from in vitro cultures for multiple Fa isolates, and this information is now being used to identify Fa metabolites from infected plant material. A combination of metabolomic and genomic analyses led to the identification of 5 potential secondary metabolite clusters as candidate virulence factors in pulse root rot as well as FHB. Given that Fa and Fg are common on both pulses and cereals in SK and AB, this new knowledge on their interactions across this spectrum of susceptible crops provides some insights into how rotations with these crops are contributing to diseases in the field. Furthermore, an understanding of pathogen virulence factors has opened the door to identification of downstream targets for breeding efforts and chemical mitigation against these two pathogens.