Sclerotinia sclerotiorum (Lib.) de Bary causes Sclerotinia stem rot on canola and many other crops of economic importance in the U.S. SSR is primarily controlled with fungicides applied at flowering time. Most fungicides currently used to control SSR can promote resistance buildup in their target populations making monitoring of sensitivity important. In this study the reaction of S. sclerotiorum to thiophanate-methyl (TM) and metconazole (MTZ) was characterized. Samples collected in several states of north central U.S. were used. Three and ten isolates were considered to be moderately insensitive to TM and MTZ, respectively. Greenhouse trials indicated, however, that diseases caused by these isolates could be effectively controlled using currently recommended doses of each compound. In vitro sensitivity to TM was temperature dependent. A previously unreported mutation at codon E111D in the β-tubulin gene of a TM-moderately insensitive isolate was identified.