Over the past twenty years, hop production has expanded in parallel with the craft brewing industry, resulting in a high-value crop with low tolerance for defect in harvested hop cones. Podosphaera macularis is an ascomycete fungus that causes powdery mildew of hop, which is arguably the most destructive disease with respect to its potential for diminishing yield and cone quality. Historically, research on P. macularis has focused largely on the asexual growth forms of the pathogen, as that is the only phase currently observed in the Pacific Northwest (PNW) US region, where over 96% of US hop production resides. As such, the epidemiology and ecology of the disease with respect to the P. macularis ascigerous stage (chasmothecia) is not well understood, even though this growth form has been reported in most hop growing regions east of the Rocky Mountain range. Furthermore, due to the difficult-to-culture obligately biotrophic nature of the pathogen, there are relatively few molecular tools available to track P. macularis population structure and movement. As such, we developed a library of 54 high-throughput, cost effective amplicon sequencing (AmpSeq) molecular markers by re-purposing an existing transcriptome dataset as the source of genetic variation. While this marker design pipeline serves as a valuable template for generating similar marker libraries for other obligately-biotrophic or otherwise difficult to culture pathogens, the project also provided valuable insight into the current population structure of P. macularis throughout the US. Genotyping results indicate that the strains of P. macularis recently introduced into commercial hop yards throughout the Midwest and Eastern US have likely arrived via infected hop planting material, which harbors a PNW US derived P. macularis strain, as opposed to introductions occurring via wind-dispersal from nearby P. macularis populations residing on feral hop. This project also created a novel set of qPCR markers for P. macularis mating type, which were used to provide an updated distribution map of P. macularis mating types within the US. This dissertation also greatly improved understanding of P. macularis overwintering potential via chasmothecia, demonstrating that early season disease incidence can reach levels of up to 70% when conditions are favorable for ascosporic infection. A pair of regressions models were developed to improve the timing at which control measures are taken during the early spring growing season, with the first model predicting the window of chasmothecial maturation based upon degree day accumulation, and the second model assigning an ascosporic infection risk level to rain events based upon the temperature and duration of the precipitation. These studies on the epidemiology of the disease indicate that existing grower practices such as spring pruning, early season fungicide applications, and basal foliage removal are likely even more crucial when the ascigerous P. macularis growth form is present within a hop yard.