Sclerotinia sclerotiorum is the causative agent of white mold and is responsible for significant yield losses in crop species across the globe, including Brassica napus (canola). To improve our understanding of the B. napus – S. sclerotiorum pathosystem, I coupled laser microdissection with global RNA sequencing, to explore global shifts in gene activity at the tissue specific level. Transcriptomic profiling of the epidermis, mesophyll and vascular leaf tissues in response to infection revealed previously uncharacterized specific and conserved roles in defense of ontogenetically distinct leaf tissue layers. Differential gene expression analysis identified defense regulators like the pattern recognition receptor PR5K that plays a role in disease susceptibility across a broad range of plant pathogens. While these experiments improved our understanding of this pathosystem, there is still a need to develop effective S. sclerotiorium control methods. RNA interference (RNAi) is a conserved cellular pathway within eukaryotes capable of silencing mRNA transcripts through sequence complementarity to double-stranded (ds)RNA molecules. RNAi can be triggered through spray induced gene silencing (SIGS) using topically applied dsRNA molecules, or host induced gene silencing (HIGS) through the generation of transgenic host plants expressing these target dsRNA molecules. In my thesis, I demonstrate the utility of both SIGS and HIGS in slowing S. sclerotiorum infection in the model plant Arabidopsis thaliana, while also exploring the influence of HIGS at the molecular level in both the host and challenging pathogen. Together, these findings provide novel insight into the host response and pathogenicity of S. sclerotiorum and demonstrate the utility of transgenic (HIGS) and non-transgenic (SIGS) applications in disease control.