Fusarium Head Blight (FHB) caused by a fungal pathogen Fusarium graminearum is one of the significant constraints to wheat production in the United States due to its reduced yield and mycotoxin contamination. The intensive application of fungicides on cereal crops, such as wheat, has led to the development of resistance in many fungal pathogens that infect them. Historically, populations of Fusarium graminearum have been mainly treated as homogeneous at the level of management and resistance breeding. However, this clashes with documented variation in populations in terms of pathogenic traits, such as fungicide sensitivity and toxin production. This work aimed to determine the variation in sensitivity of the F. graminearum NA2 population to tebuconazole and propiconazole, and to identify the genetic basis of phenotypic variation, providing targets for disease management. Sensitivity of 150 F. graminearum isolates towards the two demethylation-inhibitor (DMI) fungicides was tested using a flat-bottom 96-well plate assay. Absorbance readings were taken before incubation, and at 5 and 7 days at 405 nm. Effective concentration 50 (EC50) values were computed using R packages. We used standard statistical methods to detect associations between genetic variants derived from whole-genome sequencing and pathogen traits. Using genome-wide association studies (GWAS), we aim to identify the genetic basis of variability in fungicide sensitivity. We anticipate our results will aid in developing strategies to manage FHB outbreaks and will suggest targets for pathogen control.