Blackleg (stem canker) of crucifers is a globally important disease caused by multiple genetic subclades of the fungi Plenodomuslingam (syn.: Leptosphaeria maculans) and Plenodomus biglobosus (syn.: Leptosphaeria biglobosa). In our study, we monitored the geographical distribution of these two pathogen species from rapeseed growing areas in Hungary. Multiplex PCR identified 48.7% of the isolates as Plenodomus biglobosus, which indicates the non-recent introduction of the pathogen into Hungary. In addition, multi-locus analysis revealed low genetic diversity within the species, as all isolates were clustered to the Plenodomuslingam ‘brassicae’ and Plenodomus biglobosus ‘brassicae’ subclades. The low genetic diversity of a population generally means reduced adaptation potential, which is essential information in breeding and in developing more effective management strategies.