Many quantitative trait loci (QTL) for resistance to Fusarium Head Blight (FHB) in wheat (Triticum aestivum L.) have been identified in diverse sources worldwide. Most sources are spring wheat, such as the Chinese cultivar, Sumai 3, which has been widely used in spring wheat regions; however, in the soft red winter wheat region of the U.S., resistance in local adapted varieties is utilized predominantly in breeding programs. Two U.S. soft red winter wheat cultivars, Massey and Ernie, have moderate resistance to FHB. A set of 152 F_7:14 recombinant inbred lines (RILs), derived from the cross ‘Becker’/Massey (BM) and 236 RIL_S from Ernie/MO 94-317 (EM), were evaluated for FHB in nine environments during three years. A total of 32 QTL associated with various traits were detected from both BM and EM. Six common QTL between two populations were located on chromosomes 2BL, 2DS, 3BL, 4BS, 4DS, and 5AS. Their LOD scores ranged from 2.6 to 31.3 with R² from 3.3% to 36.5%. In addition, eight consistent QTL from BM and four consistent QTL from EM were associated with more than two traits or one trait from multiple environments. New common QTL were identified on chromosomes 2BL, 4BS, 4DS, and 5AS to increase thousand kernel weight, and the one on chromosome 4DS could decrease FDK. These QTL except the one on chromosome 2BL could increase FHB and TKW concurrently. These common QTL are of interest in breeding to enrich the favorable alleles to enhance the FHB resistance.