Analysis of quantitative trait loci (QTLs) associated with a resistance to fungal invasion within plant tissues (Type II resistance) in the case of Fusarium head blight (FHB) was conducted in doubled haploid lines (DHLs) developed form the cross Fukuho-komugi (moderately susceptible)/Oligo culm (very susceptible) using random amplified polymorphic DNA (RAPD) markers. Transgressive segregants of 26 lines with R, MR and M levels of resistance and seven lines with a VS level of resistance were detected in this population of 110 DHLs, using the parental values as standards. It is suggested that the unique configuration of resistance genes is causing the skewed distribution for Type II resistance in this cross. From the results of QTL analysis using 65 RAPD markers in the DHLs, four RAPD markers, OPZ-10₆₈₀ OPAG-18₃₄₀ OPAF-06₃₄₅ and OPW-13₄₃₅ associated with Type II resistance were identified. Three RAPD markers were linked with recombination values of 6.4 and 11.8%. These RAPD markers were individually selected by t-test. Hence, it is suggested that the specific regions of the tentatively designated linkage group c of the wheat genome are associated with Type II resistance to FHB. As a result, it may be possible to detect the latent susceptible modifier of Fukuho-komugi using three of them. Finally, the relationship between the characteristics of FHB caused by Fusarium graminearum and resistance mechanisms in wheat was analyzed based on the results of this study and data from the literature for the resistance to FHB. It is suggested that breeding strategies including pyramiding of resistance genes and introgression of additive minor genes in an adapted background may enable to make rapid progress in the breeding of FHB-resistant wheat varieties.