Recombinant inbred lines (RILs) generated from a cross between a cultivated species and its wild progenitor species serve as important germplasm for introgressing valuable genes from a wild species to a cultivated species. During this breeding process, it is equally important to prevent the loss of agronomically important genes in the cultivated species. In an effort to establish an efficient selection system for the single Rsv1 gene conferring durable resistance to soybean mosaic virus (SMV) in the soybean cultivar Hwangkeum (also known as Suweon 97), which is a parent of a RIL population from Hwangkeum (cultivated soybean) × IT182932 (wild soybean), in the present study, we unexpectedly identified an additional necrosis-conditioning gene unmasked by a recombination in the middle of the Rsv1-containing nucleotide-binding leucine-rich repeat gene cluster region and the Rsv3 gene in Hwangkeum. Thus, Hwangkeum contains at least three SMV resistance genes consisting of two tightly linked genes at the Rsv1 locus and the Rsv3 locus. The results of this study provide additional important information for use of the Hwangkeum genome in soybean breeding programmes.