Soil-borne wheat mosaic virus (SBWMV) is considered as one of the most important diseases in winter wheat in central and southeastern US. To identify quantitative trait loci (QTLs) for SBWMV resistance, two recombinant inbred line (RIL) populations were developed from two crosses Pioneer 26R61/AGS 2000 (178 lines), and AGS 2020/LA 95135 (130 lines), respectively. Pioneer 26R61 and AGS 2020 with different backgrounds were resistant to SBWMV, and AGS 2000 and LA 95135 were susceptible. For the Pioneer 26R61/AGS 2000 population, QTLs analysis was conducted with Windows QTL Cartographer based on a framework linkage map with 905 markers. One major QTL QSbm.uga-5DL was identified in all environments at a highly significant LOD value, and flanked by two co-dominant markers Xbarc161 and Xbarc177 on the distal chromosome 5DL. The two markers were closely linked with a distance of 0.4 cM. The QTL explained 58% of the total phenotypic variation for mean disease rating. In addition, the genetic map of chromosome 5D was constructed using the AGS 2020/LA 95135 population. The map included 32 loci, and was used for QTL analysis based on composite interval mapping (CIM). The same QTL, QSbm.uga-5DL, was consistently detected in the population, and was completely linked with the markers Xbarc161 and Xbarc177, and explained 38-49% of total trait variation. The linked markers Xbarc161 and Xbarc177 were validated using 100 randomly selected plants from F_2:3 families of AGS CL7/AGS 2000, and the evidence showed that the two markers were co-segregating with the SBWMV resistance gene in AGS CL7, and AGS CL7 did not have the same pedigree as Pioneer 26R61 or AGS 2020. QSbm.uga-5DL was therefore a conserved locus that conditioned SBWMV resistance on chromosome 5DL.