Sclerotinia sclerotiorum is the causal agent of Sclerotinia stem rot (SSR), which affects over 400 plant species including economically important crops. The genetic and physiological basis of partial resistance of soybean to SSR needs to be characterized before it can be incorporated effectively into new soybean cultivars. This thesis explored the physiological, anatomical and molecular characterization of the defense responses against this necrotrophic fungal pathogen observed in a susceptible cultivar OAC Shire and partially resistant cultivar OAC Salem. Measurements of area under canker progress curve, number of days for visible disease-related symptoms, stomatal conductance (gs), dry and fresh matter, and accumulation of starch grains were analyzed comparatively between the two cultivars for a period up to 12 days after inoculation. Two days after inoculation, susceptible plants exhibited significantly greater starch accumulation than partially-resistant plants. A significant increase in gs was observed in the susceptible plants only. Disease related symptoms, such as severity of wilting and number of days to plant death were significantly lower in OAC Salem than in OAC Shire. Light microscopy analyses on stem and detached leaf samples of both genotypes showed that direct penetration of the fungal hyphae through the cuticle using the base of non- glandular trichomes was observed exclusively in the susceptible cultivar. Cytoplasm disorganization and reinforced cell walls were observed in epidermal and cortical cells of OAC Salem causing a delay in tissue maceration. RNA-Sequencing analyses at several stages of infection were carried out using Next Generation Sequencing. Genes related to PAMP-triggered Immunity (PTI) were identified, including respiratory burst oxidases and mitogen activated protein kinases. In addition, other genes related to PTI such as jasmonic acid/ethylene biosynthesis and regulation were differentially expressed as well. A transient activation of those mechanisms was observed only at 3 days post-inoculation (dpi) with a shutdown of several processes at 5 dpi in the susceptible cultivar, OAC Shire. The results obtained in this thesis may contribute to a better understanding of the plant defense mechanisms against necrotrophic pathogens and lead to development of breeding strategies for incorporating partial resistance to SSR into commercial cultivars using gene expression-based markers in soybeans and potentially other hosts.