Glycine soja Siebold & Zucc. PI 393551 carries gene(s) for resistance to yellow mosaic disease, which is caused by Mungbean yellow mosaic India virus (MYMIV). Yellow mosaic disease is a serious constraint to soybean [Glycine max (L.) Merr.] production in India. However, the gene(s) imparting resistance to MYMIV in G. soja have not yet been mapped. In the present study, three F2 populations derived from crosses of the three G. max cultivars ‘Ankur’, ‘Sawarn Vasundhra’, and ‘JS335’ with PI 393551, the donor for MYMIV resistance, were phenotyped for reaction to MYMIV at the geographic hot spot for yellow mosaic disease to determine inheritance of MYMIV resistance in PI 393551. All three F2 populations exhibited a 15:1 ratio of individuals resistant and susceptible to MYMIV, indicating duplicate dominant inheritance of MYMIV resistance genes. Further, a large F2 population (1520 plants) reconstructed from JS335 × PI 393551 was used for mapping MYMIV resistance genes. Bulked segregant analysis identified two genomic regions associated with MYMIV resistance, one on chromosome 8, and another on chromosome 14. A total of 78 plants with 100% MYMIV infection, which were expected to be homozygous for recessive genes, were genotyped using polymorphic simple sequence repeat (SSR) markers near linked markers on chromosome 8 and 14. Genetic analyses revealed tight linkages of MYMIV resistance with SSR marker BARCSOYSSR_08_0867 (15,434,295 bp) on chromosome 8, and with BARCSOYSSR_14_1416 (47,686,933 bp) and BARCSOYSSR_14_1417 (47,738,940 bp) on chromosome 14. The identified SSR markers that are tightly linked to MYMIV resistance genes will be useful for introgression of MYMIV resistance from G. soja into G. max.