The electrophoretic karyotype of 11 strains of the phytopathogenic fungus Septoria nodorum has been established by pulsed field gel electrophoresis with the CHEF DRII system. Each strain had a similar overall karyotype with 14-19 chromosomes being resolved in the size interval between approximately 0.5 and 3.5 megabase pairs (Mb). However, there were clear differences in karyotype both between and within groups of strains adapted to wheat or to barley. Considerable karyotype variation was apparent even among 6 wheat-adapted strains isolated from the same population. Only 2 strains possessed identical karyotypes; these were isolated from the same leaf and were heterokaryon-compatible and are probably independent isolates of the same clone.