Isolates of Leptosphaeria maculans, the fungus that causes blackleg of canola, were randomly sampled from seven sites in both eastern Australia and Western Australia. Amplified fragment length polymorphism and restriction fragment length polymorphism analyses showed a low degree of genetic differentiation between isolates of L. maculans from these sites. There were small, weakly significant differences in genetic diversity of isolates when grouped according to the cultivar, age of the plants and the region from which the isolates were sampled. However, distinct populations were not observed. There was an even distribution of mating types, as shown by a PCR assay using idiomorph-specific primers.