The spread of fungicide resistant and/or tolerant phytopathogenic fungi is an important factor affecting crop protection. However, the mechanisms of fungal response to fungicide application are not entirely characterised. In particular, the contribution of previously known resistance factors and the final influence of fungicide treatments on metabolism of surviving mycelia (e.g. mycotoxin increased release and biosynthesis potentially causing contamination of the crops) merit investigation, in order to improve future molecular diagnostics of fungicide resistant strains. The performed experiments have shown distinct expression changes for homologs of a known fungicide resistance factor Flr1 (yeast; DHA1 family of major facilitator superfamily transporters) after azole application in cultured fusaria. Two distantly related homologs of that gene were selected, based on the unsupervised clustering and phylogenetic analysis of transporter sequences. One of these (FGSG_02865), was found to occur across the Fusarium sambucinum complex (F. graminearum, F. culmorum, F. cerealis) and was upregulated starting 24 h after fungicide treatments. This delayed response may point to possible involvement of DHA1 antiporters in a generalised response to stress resulting from fungicide treatment. Additional expression profiling was conducted for the mycotoxin biosynthetic genes (trichothecene and zearalenone gene clusters) in strains of Fusarium sambucinum complex cereal pathogens. The expression changes, when subjected to treatment with the fungicides (flusilazole, carbendazim), show that even an effective treatment (in this study, the benzimidazole fungicide carbendazim) applied to the grown mycelium, can result in enhanced activation of mycotoxin biosynthetic genes in fungal cells which survive the treatment. Our results suggest that increased mycotoxin contamination can be strongly influenced not only by the amount or the type of antifungal compound, but also the timing of fungicide exposition (stage of infection).