Soybean mosaic virus (SMV) is one of the most destructive viral diseases in soybean [Glycine max (L.) Merr.]. Three loci for SMV resistance have been identified in soybean germplasm and used in breeding programs. The objective of this research is to identify PCR-based markers associated with the allele(s) for resistance to SMV in J05 soybean. J05 is a Chinese soybean cultivar, which is resistant to all seven SMV strains in the U.S. The resistance to SMV strain G1 in J05 was controlled by a dominant gene (Rsv1) on MLG F. Three SSR markers, Satt114, Satt510+Sat_317, and Sat_154+Sat_317, and one PCR-based marker Rsv1-f/r were identified to be associated with the Rsv1 gene. The resistance to SMV strain G7 in J05 was controlled by another dominant gene (Rsv3) on MLG B2. Three SSR markers, Satt726, Sat_424, and M3aSatt were identified to be associated with Rsv3. These PCR-based markers can provide breeders with a useful tool in selection and pyramiding of the two independent genes for SMV resistance in J05.