Rhizoctonia root and hypocotyl rot, caused by Rhizoctonia solani Kühn [teleomorph Thanatephorus cucumeris (Frank) Donk], is an important disease of soybean [Glycine max (L.) Merr.]. Planting resistant cultivars would be an effective and environmentally sound strategy to minimize economic losses from this disease. To facilitate developing resistant cultivars, a study was conducted to: (i) investigate inheritance of resistance to Rhizoctonia root and hypocotyl rot in the moderately resistant soybean PI 442031, and four moderately susceptible commercial cultivars and (ii) identify simple sequence repeat (SSR) markers associated with resistance to Rhizoctonia root and hypocotyl rot. Genetic analysis of several segregating populations indicated that resistance to Rhizoctonia root and hypocotyl rot in soybean was quantitatively inherited and controlled by both major and minor genes with additive gene effects. The estimates of broad sense heritability of resistance were low to moderately high. Transgressive segregants with enhanced levels of resistance were developed by crossing adapted but moderately susceptible commercial soybean cultivars. Three SSR markers (Satt281, Satt177, and Satt245) were significantly associated with host resistance in both F₂ and F_4:5 populations of PI 442031 × Sterling, wherein both parents contributed resistant alleles. This is the first report on mapping of Rhizoctonia root and hypocotyl rot resistance genes in soybean. Our results indicate that marker assisted selection, coupled with phenotypic selection in later generations, should help to facilitate the development of soybean cultivars resistant to Rhizoctonia root and hypocotyl rot.