Many biotic factors can negatively affect cereal grain quality and safety, including fungal damage due to Fusarium Head Blight (FHB). FHB can be caused by many different species of Fusarium, some of which produce trichothecenes, such as deoxynivalenol or DON. Trichothecenes are of particular concern due to their regulation and toxicity to humans and livestock. However, Canada has a robust grain grading and monitoring system to ensure fungal and toxin contamination remains within acceptable levels and that Canadian wheat meets the quality and safety requirements of domestic and export markets. Since 1995, our harvest monitoring program has assessed the occurrence and severity of Fusarium Damaged Kernels (FDK) in wheat for over 200,000 harvest samples. The results of our monitoring identified regional and temporal differences in the fungi, with the occurrence of FDK having increased over time, particularly within the last decade. Traditional methods of Fusarium species identification involved culturing and manual inspection through microscopy, which is low throughput, laborious, and can not provide information on the toxin potential of the fungi. Using high-throughput DNA testing, we have assessed the Fusarium species and toxin chemotypes for fungi in over 40,000 FDK, allowing us to increase our testing capacity and provide robust data on shifts in the pathogen populations and risks for trichothecene occurrence. To complement our DNA testing, we have also developed new biochemical fingerprinting tools and databases, Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS), that can be used for fungal identification and biotyping. Our monitoring dataset is one of the largest of its kind, and provides valuable information on trends on FDK spanning the last 28 years.