A major QTL (quantitative trait locus) for Fusarium head blight (FHB) resistance, Qfhs.ndsu‐3BS, derived from ‘Sumai 3’, has been identified and verified by several research groups via molecular marker analysis. Further study of this QTL is worthwhile because it explains a large portion (25–60%) of the variation in FHB resistance in the reported studies. The objectives of this study were to (i) identify additional molecular markers for Qfhs.ndsu‐3BS, (ii) construct a cytologically based physical map of chromosome 3BS, and (iii) identify germplasm with novel FHB resistance genes with SSR markers near Qfhs.ndsu‐3BS Two new simple sequence repeat (SSR) markers (XBARC133 and XBARC102), two sequence tagged site (STS) markers (XSTS3B1 and Xsun2), and one restriction fragment length polymorphism (RFLP) marker (Xfbb185), were mapped to the Qfhs.ndsu‐3BS region. On the basis of deletion line analysis, this major QTL is likely located on the deletion bin 3BS 0.78‐0.87. Fifty‐four FHB resistant lines from throughout the world and 20 North American spring wheat (Triticum aestivum L.) lines of historical prominence were genotyped by five SSR markers (Xgwm389, Xgwm533, XBARC133, Xgwm493, and XBARC102) associated with Qfhs.ndsu‐3BS The Sumai 3 haplotype is rare. Only 25 out of 54 FHB resistant lines and one North American spring wheat line have Sumai 3‐type alleles for at least one of these five SSR markers. Twelve FHB resistant lines have the same SSR allele as Sumai 3 for at least four of the five SSR markers, and therefore most likely contain this major QTL. The other 42 FHB resistant lines may carry novel FHB resistance genes, and are worthy of further genetic study.