Stagonospora nodorum isolates were collected from the Western Australian grain-belt during 1993. These isolates and a subset of isolates taken from a single location were used to assay the level of variation within the pathogen population. The isolates were compared using anonymous nuclear DNA markers. Three low copy-number and a single high copy-number RFLP probe were used to generate polymorphisms. The collection exhibited a high genotypic diversity for the high copy-number probe, a result consistent with the high level of sexual reproduction previously found in the fungal population. The high level of genotypic diversity was consistent with previous international studies. There was no evidence of differentiation between the total collection of isolates and the subset of isolates taken from the single location. Further work needs to be undertaken to determine if the aggressiveness of the pathogen is influenced by the host genotype.