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Fusarium head blight (FHB) caused by Fusarium graminearum, the FHB-associated mycotoxin deoxynivalenol (DON), and foliar fungal diseases are significant threats to wheat production. This research 1) evaluated the effects of fungicide chemical class, application timing, and cultivar resistance on FHB and DON under field conditions; 2) evaluated the effects of field-applied fungicide chemical class, grain moisture, and time on DON under grain storage conditions; 3) evaluated the effects of field-applied fungicide chemical class and time on trichothecene-related gene (Tri5) expression under grain storage conditions; 4) determined the optimum F. graminearum spore concentration and spike bagging period following inoculation for accurately discriminating between FHB resistant and susceptible wheat cultivars under greenhouse conditions; and 5) determined the optimum timing of fungicide applications for control of foliar fungal diseases of wheat under field conditions. A triazole fungicide controlled FHB and DON more effectively than a strobilurin fungicide. A triazole applied 6 days after anthesis was as effective as an anthesis (standard timing) application, indicating a wider window of application for growers’ needed flexibility. In storage, DON decreased over time in grain of a moderately resistant cultivar treated with a triazole and increased in grain of a susceptible cultivar treated with a strobilurin. During storage, DON biosynthesis Tri5 gene expression increased over time during storage of high grain moisture grain, a significant reduction in the relative expression of the Tri5 gene and a downregulation of the gene occurred in the triazole treatment whereas expression of the gene increased in the strobilurin treatment. In the greenhouse, lower concentrations of F. graminearum inoculum (6.25 x 103 and 1.25 x 104 spores/mL) were more efficient in discriminating between a moderately resistant and a susceptible wheat cultivar compared to the standard concentration (1 x 105 spores/mL). The optimum spike bagging period following inoculation for discrimination between a moderately resistant and a susceptible cultivar was 48 hours or 72 hours (the standard). Foliar fungicide applications in field plots at the flag leaf and boot growth stages of wheat were more effective in protecting yield than later applications. Results from this research will enhance knowledge in the epidemiology and management of FHB, DON, and foliar fungal diseases of wheat. Advisors: Stephen N. Wegulo and Heather Hallen-Adams