Northern corn leaf blight (NCLB) is a devastating fungal disease of maize and caused by the fungal pathogen Setosphaeria turcica. We show by sequencing of S. turcica isolates and evolutionary modeling that over the last 30 years different clonal, asexually reproducing lineages of the pathogen emerged and spread throughout Central and Western Europe. This likely resulted from an expansion of the cultivation area and modern agricultural practices, we do not find evidence that strong selection was a major driver of the development within clonal lineages. New pathogen races, which are virulent to single resistance genes used in maize breeding, seem to have evolved independently within different clonal lineages by spontaneous mutations.