Fusarium head blight (FHB) is one of the most serious diseases of wheat. FHB reduces grain yield and quality, and the fungus produces mycotoxins, such as deoxynivalenol (DON). In addition to exotic sources of FHB resistance, sources of resistance in adapted wheat lines are commonly used in wheat breeding programs in North America. The objective of the current study was to identify and compare QTLs associated with FHB related traits in Canadian Eastern doubled-haploid (DH) winter wheat populations (Vienna/25R47 and Maxine/FTHP Redeemer), which parents are registered for Ontario, Canada. Each population was spray inoculated with a combined suspension of macroconidia of Fusarium graminearum isolates at 50% anthesis at multiple environments. FHB symptoms were recorded as severity (the percent spikelets infected) and incidence (the percent heads infected) and a FHB index was calculated. The harvested grain was analyzed for DON level using ELISA method. Plant height and heading dates were also recorded. Genotyping was performed using DArT markers. JoinMap® 4.1 was used to create the linkage map and MapQTL® 6 was used for QTL analysis. QTL associated with FHB resistance in the Vienna/25R47 population were identified on chromosomes 4B (9.8-15.8% explanation) and 4D (17.2-18.4% explanation), which were also associated/linked with Rht-B1 and Rht-D1 semi-dwarf genes. QTL on chromosome 2D (9.7-29.6%), 4B (16.3-23.1%) and 4A (7.2-11.4%) explained most of the variation for severity, incidence, index, DON level and plant height in the Maxine/Redeemer population, indicating the possible presence of the dwarf alleles on Rht-B1 and Rht8 loci in the present population. The 2D QTL was also associated with heading date (53.7-59.6% explanation). The lines with the tall allele on the 2D QTL (Rht8), combined with the short allele on the 4B QTL (Rht-B1) and the FHB resistant allele on 4A QTL showed the best genetic combination to obtain short and early maturing plants with good resistance to FHB and low DON. Common QTL, associated with FHB resistance, across the populations was 4B. The results indicate that progenies, with good FHB resistance, are identified faster by using DH technology, adapted sources of FHB resistance and marker assisted selection (MAS).