Resistance to Fusarium head blight (FHB) is complex and involves multiple genes with relatively small effects. The breeding line 32C*17 did not carry the widely known Fhb genes (Fhb1, Fhb2, and Fhb5), but still showed strong FHB resistance under severe disease pressure in both Canada and Germany. A double haploid (DH) population (3CPR) was generated from the cross between 32C*17 and the cultivar Peregrine with intermediate FHB resistance. Another DH population (PR3C) was created from the reciprocal cross. The objective of this study was to identify quantitative trait loci of FHB resistance and other agronomic traits associated with FHB resistance. The efficiency of marker-assisted selection (MAS) based on the detected strong FHB QTL in the 3CPR population was estimated in its reciprocal population PR3C. Six site-years of field tests and one year of greenhouse testing of the 3CPR population were conducted to collect data for disease incidence (Inc), severity, Fusarium damaged kernels and deoxynivalenol (DON), plant height and flowering date. Genotyping of both the 3CPR and PR3C populations was conducted with the 90K wheat Illumina Infinium iSelect SNP array platform. Linkage maps of both populations had good genome coverage. Transgressive segregation in the 3CPR was observed for all FHB traits measured. Several FHB QTLs were detected, but were not consistently shown through all site years. Both parent lines carried the wild type allele in the semi-dwarfing locus Rht-B1, but had a minor height difference, resulting in two height QTL. The 32C*17 alleles reduced Inc and DON for QTL identified on chromosomes 4D and 6D. The distance between the 4D QTL and the Rht-D1 locus was 10-12 cM in the linkage map and approximately 450,358,490 bp in the physical map, thus the 4D FHB resistance was not directly affected by the Rht-D1 locus. Peregrine showed intermediate field severity (32.6%) and high greenhouse severity (75.3%), but contributed resistance to disease spread (severity) base on QTL identified on chromosome 3A in both field and greenhouse tests. This study revealed that the FHB resistance of 32C*17 was mainly resistance to initial infection (Type I). The PR3C population will be used to validate the potential value of the 4D and 6D QTL for marker-assisted selection.