Understanding the ability of the plant microbiome and its ability to aid in biotic and abiotic stress response is an emerging topic of research. This approach may offer new insight on plant disease management. Fusarium head blight (FHB) is a disease caused by Fusarium graminearum that affects wheat and barley worldwide. This disease reduces grain quality by contamination with the mycotoxin deoxynivalenol (DON). We considered that members of the microbiome with the potential to inhibit FHB could be identified based on differential enrichment in the barley spike during disease. Moreover, if the same taxa respond to plant genotype, that would indicate the potential for using breeding to manipulate the barley spike microbiome in a beneficial manner. We analyzed the composition of the barley spike microbiome during FHB disease onset roughly three weeks after heading in ten genotypes from a breeding population at FHB misted nurseries across four locations in the United States: ID, MN, ND and NY. Bacterial groups were identified using 16S amplicon sequencing and were analyzed for their responsiveness to both FHB disease and barley genotype. Barley genotype had a significant effect on bacterial community composition at each location, while disease had a significant effect only in the St. Paul, MN which had the highest disease severity. There was also a significant genotype by disease effect at 3 locations: ND, ID and MN. Each location also had several taxa present that are known to have members that are plant-beneficial organisms including Pantoea, Pseudomonas, and Sphingomonas, among others. The results of these experiments will help highlight the potential for barley genotypes to recruit beneficial microorganisms in response to diseases like FHB.