Cercospora leaf spot (CLS), caused by the fungal pathogen Cercospora beticola, is the most destructive foliar pathogen of sugar beet (Beta vulgaris). Located on the Minnesota and North Dakota border, the Red River Valley (RRV) is the top growing region for sugar beet in the United States. Sugar losses due to CLS in the RRV can be devastating as a result of foliar destruction by this fungus and subsequent biomass loss of the sugar beet root. We sampled leaves of CLS-resistant and -susceptible cultivars grown in a single field in the RRV to monitor changes in the phyllosphere microbiome over the growing season. CLS-resistant and -susceptible sugar beet varieties were allowed to naturally acquire CLS. Leaves from both genotypes were harvested every three weeks beginning at symptom development of the CLS-susceptible variety and ended during harvest. The full 16S rDNA gene was sequenced for each sample to characterize the leaf bacterial microbiome. Bacterial communities were profiled, and composition and predicted functions were compared between sugar beet genotypes. By monitoring communities for taxa associated with the presence or absence of CLS, we can make associations that can inform better management of CLS in an ever-changing environment.