Soybean mosaic virus (SMV) disease is one of the major soybean diseases widely distributed in soybean production areas in China. SMV strain SC13 is among the major strains occurring in northern China. In order to broaden the germplasm of soybean resistant to SMV, the inheritance mode of resistance of wild soybean ZYD03715, a core germplasm material of soybean in China, against SMV strain SC13 was studied. The allelic relationship between the resistant germplasm of cultivated soybean and the resistance loci against the same strain was determined, and the resistance genes were marked and mapped. The results showed that the resistance of the wild soybean ZYD03715 against SMV strain SC13 was controlled by a pair of recessive genes, whereas the resistance of the broad-spectrum resistant germplasm ‘Kefeng 1 Hao’ was controlled by a pair of dominant genes, and the resistance genes carried by the two resistant germplasms were nonallelic. Through the bulked segregant analysis, the resistance loci (rySC13,) of the wild soybean ZYD03715 against SC13 were located on soybean chromosome 14 (B2 linkage group), on the side of two SSR markers Satt 416 and Satt 083, with genetic distances of 4.1 cM and 0.9 cM, respectively. The resistance gene ( RkSC13) carried by ‘Kefeng 1 Hao’ was mapped between Satt 558 and Sat_254 markers on soybean chromosome 2 (D1b linkage group) by using F2 population of ‘Kefeng 1 Hao’ × ‘Nannong 1138-2’, with genetic distances of 3.7 cM and 16.1 cM. In the past, it was found that the SMV-resistance of soybean was controlled by a pair of dominant genes. In this study, recessive resistance genes were identified in wild soybeanand marked and mapped. It will lay a foundation for molecular marker-assisted selection and fine mapping and cloning of resistance genes in soybean breeding for disease-resistance.