The aggressiveness of a pathogen is the quantitative variation of disease signs and symptoms on a susceptible host. Effective use of disease resistance relies on understanding the pathogen’s potential to evolve and overcome resistance. Increased pathogen aggressiveness is less likely to diminish the effectiveness of quantitative resistance compared to qualitative resistance. There is also more understanding on the evolution of pathogen races in gene-for-gene systems of resistance. It is not fully understood how quantitative host resistance affects pathogen aggressiveness creating a need to better comprehend the population biology of plant pathogens. One theory is that resistance is selecting for aggressiveness. The pathogen must be more aggressive to overcome resistance while aggressiveness compensates for lowered reproduction. Another theory is that a susceptible host allows for higher pathogen genetic variance, leading to rapidly increasing aggressiveness through selection and competition. Fusarium graminearum causes Fusarium Head Blight (FHB) in wheat, producing significant yield losses and mycotoxin contamination. We hypothesized that the wheat’s level of resistance is selecting on the F. graminearum populations for isolate aggressiveness. Thirty-one isolates from highly susceptible and 26 isolates from moderately resistant wheat lines were used. The isolate’s aggressiveness was measured by AUDPC that was calculated from three disease severity ratings, visually damaged kernels, and deoxynivalenol contamination. DNA was extracted and sequenced to create a SNP data set that was used to perform a whole-genome scan for selection and a phylogenetic analysis. The results of this research found that the population of F. graminearum from susceptible wheat had more aggressive isolates. This led to the conclusion that resistant wheat varieties have not selected for a population with primarily aggressive isolates but mixed levels of aggressiveness. The population of isolates from highly susceptible wheat were primarily aggressive suggesting that on a susceptible host aggressive isolates might be outcompeting weaker isolates. The level of wheat resistance added selection pressure to the F. graminearumisolates as both populations had unique regions of the genome and genes under selection. The fixed level of isolate aggressiveness and the increased number of genes under selection suggests that there is stronger selection pressure occurring in the population from highly susceptible wheat. These results indicate that host resistance will be a durable and long term solution to FHB on wheat.