Fusarium head blight (FHB) is one of the most harmful diseases affecting cereal crops. Polyphenols provide a protective effect against biotic and abiotic stresses. It is therefore interesting to focus on genotypes with a high concentration of these compounds in the aleurone and pericarp. This research examines the interaction between five different pigmented wheat cultivars (Purendo, Skorpion, Rosso, Vanilnoir and Indigo) and the fungal pathogen Fusarium graminearum. Data obtained from phytopathological experiments and AUDPC calculation, demonstrate that blue aleurone genotypes are highly sensitive to FHB while genotypes with purple pericarp are less sensitive. Notably, Vanilnoir demonstrated a disease incidence identical to the resistant control Sumai3 (less than 10% after 21 days of infection). FDK evaluation and the total phenolic content showed no differences between genotypes. Furthermore, the quantification of the fungal genome by RT-qPCR showed that the pathogen had a lower diffusion in the Vanilnoir cultivar (compared to the more vulnerable varieties such as Skorpion), suggesting the involvement of a type II resistance mechanism. As a further level of investigation, a transcriptomic (mRNAseq) experiment was performed on the Vanilnoir and Rosso cultivars with the aim of identifying genes involved in the mechanisms of SAR induction at 2 days after infection.