Stemphylium leaf blight (SLB), caused by the fungus Stemphylium vesicarium, is one of the most important foliar diseases affecting onions (Allium cepa L.) in the northeastern United States. SLB can substantially reduce yield due to the premature defoliation that results in smaller bulbs. Management strategies to control SLB involve cultural and chemical practices that are targeted to reduce the rate of disease progress. However, fungicide resistance development, the absence of resistant onion cultivars to SLB, and the lack of knowledge surrounding inoculum sources, impose great challenges in the design of sustainable management strategies. To address this, the effect of inoculum sources such as onion transplants and volunteers on SLB epidemics in New York (NY) was characterized through population biology analysis. Our results indicated that S. vesicarium from infected transplants contributed minimally to NY SLB epidemics, while volunteer onions served as an important inoculum source. Population genetics analysis also showed substantial genetic differentiation between S. vesicarium populations from onion fields in NY and Georgia, with more uniform haplotype distributions within each state and distinct clustering between them. The genomic basis of tebuconazole resistance was studied using a multitool genomic approach, where results suggested that resistance may be governed by one or a few major genes, based on a bimodal sensitivity distribution. No mutations in the target gene SvCYP51 were associated with resistance, suggesting that alternative mechanisms might be involved. Population differentiation analysis identified two candidate genomic regions, including a gene encoding for an amino acid transmembrane transporter, but further studies are necessary to corroborate their association with resistance to tebuconazole in S. vesicarium. Controlled environment and field trials identified onion cultivars ‘SVNY1610’, ‘SVNY1608’, ‘Red Bull’, and ‘Redwing’ as having reduced susceptibility to SLB. Red onion cultivars showed a trend toward lower susceptibility than yellow cultivars, although further validation is needed. Overall, this dissertation supports more sustainable strategies for managing SLB in NY onion production and advances the understanding of the pathogen’s population biology and epidemiology. The findings also provide a framework for future research and disease management efforts in other onion producing regions, supporting integrated approaches at a broader national scale.