Technical Abstract: Sclerotinia stem rot of soybean [Glycine max (L.) Merr.], caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a difficult disease to manage, although some gains have been made through breeding for quantitative resistance. The objective was to map quantitative trait loci (QTL) controlling partial resistance to Sclerotinia stem rot from the soybean plant introduction (PI) 194639. The resistance QTL were mapped in a population of 155 F4:5 recombinant inbred lines (RILs) developed from the hybridization of the partially resistant parent, PI194639, to the susceptible cultivar Merit. The population was evaluated for Sclerotinia stem rot resistance using a cut stem inoculation technique and was genotyped with 134 simple sequence repeat (SSR) markers. Broad-sense heritability of lesion length (LL) after inoculation with the cut stem technique in the population was 0.57. Two putative QTL controlling LL were identified by composite interval mapping (CIM) and these mapped onto linkage groups (LGs) A2 and B2. The LG A2 QTL was tightly linked to the marker Sat_138 and explained 12.1% of the phenotypic variation for LL. The LG B2 QTL was proximal to the marker Satt126 and explained 11.2% of the phenotypic variance. These results suggest that SSR markers associated with resistance QTL mapped in this study for Sclerotinia stem rot resistance may be useful for marker-assisted breeding programs in soybean.