Achieving high Fusarium head blight (FHB) resistance is an ultimate goal in any wheat breeding program to secure grain yield and avoid mycotoxin contamination of the harvest. Despite great efforts by breeding companies, the gain from selection was negligible in the last 20 years in Central Europe. Quantitatively resistant cultivars are available, but there are only few of them, they have a low acreage, and are often unfavourable for agronomic characters. Besides a complex inheritance, the main cause for this is the complex interactions between FHB resistance, plant height, and anther retention. In the high-input wheat production in Central Europe, semi-dwarf genotypes are indispensable, accounting for >70% of all varieties. It is known that FHB resistance shares pleiotropic loci with plant height (PH) and anther retention (AR). The dwarfing gene Rht-D1b (Rht1) increase FHB susceptibility, whereas Rht24 is FHB neutral (Miedaner et al. 2022). Also, plant height per se has an effect with taller genotypes being more resistant (r= ‒0.42, P<0.001). The main objective of this study was to dissect the effect of morphological traits on FHB resistance. We combined correlation and path analyses, genome-wide association studies (GWAS), and genomic prediction (GP, Akohoue et al. 2022). High genotypic correlation (r_g=0.74) and direct path effect (0.57) were detected between FHB severity and anther retention (AR). A moderate correlation (r_g= ‒0.55) was found between FHB severity and plant height (PH) with a high indirect path via AR (‒0.31). Single-trait GWAS identified 25 quantitative trait loci (QTL) for FHB severity, PH and AR, while multi-trait GWAS detected six QTL across chromosomes 2A, 4D, 5A, 6B and 7B conveying pleiotropic effects on the traits. Rht-D1b was associated with high AR and FHB susceptibility with a negatively pleiotropic effect. The use of GP for selecting the genomic background was more effective than selection based on GWAS-detected markers. Strategies for the selection of semi-dwarf varieties with higher FHB resistance include (1) selection of cleistogamous wheat genotypes (AR >96%), (2) use of several FHB-neutral Rht genes, or (3) use of genomic-estimated breeding values for the selection of semi-dwarf genotypes with a high FHB resistance background.