Fusarium head blight (FHB) is a devastating fungal disease threatening wheat production worldwide. Utilization of resistant wheat cultivars is generally considered as the most effective, economic and environmental friendly approach for management of the disease. This research aimed to identify and map quantitative trait loci (QTL) for FHB resistance in two spring wheat lines (ND2710 and PI 277012) and two durum wheat lines (10Ae564 and Joppa). Using a mapping population consisting of 233 recombinant inbred lines (RILs) from a cross between ND2710 (with FHB resistance derived from Sumai 3) and the spring wheat cultivar ‘Bobwhite’ (susceptible to FHB), four QTL (Qfhb.ndwp-3B, Qfhb.ndwp-6B, Qfhb.ndwp-2A, and Qfhb.ndwp-6A) were mapped on chromosomes 3B, 6B, 2A, and 6A, respectively, in ND2710. Qfhb.ndwp-3B and Qfhb.ndwp-6B were mapped to the same genomic regions as Fhb1 and Fhb2, confirming that they originated from Sumai 3. Two FHB resistance QTL, Qfhb.rwg-5A.1 and Qfhb.rwg-5A.2, were previously identified on chromosome 5AS and 5AL, respectively, in PI 277012. In this study, Qfhb.rwg-5A.2 was delimited in a 1.09-Mbp genomic region, and DNA markers tightly linked to Qfhb.rwg-5A.2 were developed using 947 RILs from the cross between PI 277012 and Grandin (susceptible to FHB). Using a mapping population consisting of 205 RILs from the cross between the durum cultivar Joppa and the durum wheat line 10Ae564 (with FHB resistance derived from PI 277012), one QTL (Qfhb.ndwp-2A) on chromosome 2A from Joppa and two QTL (Qfhb.ndwp-5A and Qfhb.ndwp-7A) each on 5A and 7A from 10Ae564 were detected. Qfhb.ndwp-5A was mapped to the same genomic region as Qfhb.rwg-5A.2 on 5AL, and thus confirming that this QTL was derived from PI 277012. The DNA markers closely linked to the FHB resistance QTL identified in two spring wheat lines and two durum wheat lines will be useful for marker-assisted selection of FHB resistance in wheat breeding programs.