Sclerotinia stem rot or white mold (WM) [Sclerotinia sclerotiorum (Lib.) de Bary] is an important fungal disease affecting soybean [Glycine max (L.) Merr.] and causes yield and quality losses. WM is prevalent in cool and moist environments, particularly in the soybean growing regions of Northern United States and Canada. Although sources of complete resistance have not yet been identified, several quantitative trait loci (QTL) for partial resistance have been reported but generally using bi-parental mapping populations. Genome-wide association (GWA) studies have been used to dissect complex disease resistance traits in plants and to identify the genes controlling the expression. WM was assessed in 465 diverse plant introduction accessions from the USDA Soybean Germplasm Core Collection and GWA and epistatic interaction analysis was performed using 36,105 SNPs from the SoySNP50K Illumina Infinium BeadChip to 1) discover sources of WM resistance, 2) identify SNPs associated with WM resistance, and 3) determine putative candidate genes for WM resistance. Phenotyping for WM was done under artificial epiphytotic conditions in both field and greenhouse environments. Forty-five main effects and 18 epistatic interactions associated with WM resistance were identified at different growth stages and for multiple response variables. Together, these explained 7-36% of the phenotypic variation. A wide range of candidate genes were identified at the proximity of peak SNPs, which included a few disease response genes previously reported in the literature. The mode of resistance within these candidate genes varied greatly and included functions such as cell wall structure, hormone signaling, and sugar allocation, revealing the complex nature of WM resistance. Several accessions expressing resistance in all environments were identified.