Background Multidrug resistance has been identified in the fungal pathogen responsible for Septoria leaf blotch, Zymoseptoria tritici , since 2011. It has been linked to the overexpression of the gene encoding the MFS1 transporter due to inserts in the promoter region of MFS1 (P MFS1 ), namely types I-III. Recently, two new inserts were discovered in P MFS1 that were not linked to MDR, interrogating about whether P MFS1 inserts are the only drivers of MDR in Z. tritici . The goal of our study was to gain a more complete view of MDR in Z. tritici by examining the genotypic diversity associated with the MDR phenotype in a large sample of the modern population. Results We isolated 384 potential MDR strains between 2020 and 2021 in northern Europe for P MFS1 genotype and MDR assessment. We discovered six new inserts in P MFS1 , bringing the total count to 13 including one insertion-deletion in the 5’ UTR region. Of these, 11 display similarities with transposable elements, and 3 are not linked to MDR. Some field strains were significantly more resistant than their respective reference of the same P MFS1 genotype and some strains without insert displayed MDR phenotype. Conclusion We described the landscape of the MDR in modern Z. tritici population and postulate that P MFS1 is a hot-spot for insertions involving transposition events. Our study shows that MDR cannot be solely explained by inserts found in P MFS1 , and that additional mechanisms might be at work.