Septoria leaf blotch, caused by the fungus Mycosphaerella graminicola, is the most important wheat disease in Northwestern Europe, and is currently controlled by fungicide applications. Since the spread of resistance to methyl benzimidazole carbamates (MBCs) and quinone outside inhibitors (QoIs) in European countries, reliable control is mainly dependent upon sterol 14 alpha-demethylation inhibitors (DMIs). In the last decades however, a slow shift towards reduced sensitivity of M. graminicola to DMIs has been observed. This shift is caused mainly by mutations in the CYP51 gene encoding the 14 alpha-demethylase target protein for these fungicides. In this work, M. graminicola isolates were sampled at fields spread over Flanders, Belgium. In vitro assays were used to analyze the sensitivity of the Flemish M. graminicola population towards different DMIs. Sequencing of the CYP51 gene of these isolates allowed us to identify and map the haplotypes in this population. The results showed that there is a large variability in DMI sensitivity between the isolates, even within one field, which is reflected in a high diversity in CYP51 haplotypes within the M. graminicola population in Flanders. Next to some haplotypes that were not described in literature before, we found that the population is dominated by CYP51 haplotypes which were previously associated with increased resistance towards DMIs.