While winter squash or pumpkins and rhubarb are distinct and unrelated crops, both are important for the vegetable industry in New York and the Northeast United States. Their production also presents unique disease management challenges. In this dissertation, several tools were applied to address disease-related questions for both crops. Chapter 1 introduces Cucurbita spp. that are commonly grown in the US as well as current questions about the management of a common disease, cucurbit powdery mildew (CPM). In Chapter 2, biorational fungicides were evaluated for their efficacy against CPM on C. pepo. Over two years, copper-based fungicides most effectively reduced disease severity, followed by two products based on fermented bacteria and plant extracts. In Chapter 3, C. moschata breeding lines harboring the CPM resistance gene Pm-0 were evaluated for their CPM resistance and canning quality. Fruit from each breeding line were puréed and canned, and their physiochemical qualities were compared to the parental lines and a commercial standard. Fruits from the two most resistant breeding lines resembled the commercial standard, indicating that CPM-resistance has been bred into a commercially promising C. moschata background. In Chapter 4, three effective fungicides evaluated in Chapter 2 were assessed for their ability to manage CPM on the two resistant breeding lines identified in Chapter 3. Results suggested that host resistance played a larger role than fungicide treatment in reducing CPM disease severity. Chapter 5 reviews our current understanding of rhubarb cultivation and highlights future research needs to support its successful production in North America. In Chapter 6, the population biology of a rhubarb leafspot pathogen, Didymella rhei, was explored. A genotyping-by-sequencing analysis found the same genotype in every sampling location, suggesting a lack of regional differences. This raised a hypothesis that clonal propagation of the host distributes D. rhei. In Chapter 7, a new fungal species identified from R. japonica was described. The organism, named D. polygonacearum, is a close relative of D. rhei and is capable of infecting rhubarb. Finally, in Chapter 8, the presence of previously unreported viruses in rhubarb was confirmed. Tomato ringspot virus (ToRSV) was identified in a single accession in the rhubarb collection at Cornell AgriTech, prompting the determination of the collection’s virome via high-throughput sequencing. Results found six viruses in the collection. The presence of two viruses, ToRSV and beet curly top virus (BCTV) was confirmed via RT-PCR and PCR, respectively. These findings have implications for the propagation of virus-free material and distribution of germplasm in a primarily clonally propagated crop.