Isozymes of five Australian Ganoderma species were studied using cellulose acetate gel electrophoresis (CAGE) and PAGE. Phenetic analysis supported the distinction between the five species, which were separated by unbiased genetic distances of between 0.532 and 3.330. Estimates of heterozygosity and polymorphisms identified considerable genetic variability within populations and species. The putative saprotrophic G. australe, G. incrassatum and G. cupreum had the lowest genetic variability while the pathogen Ganoderma sp. Group 6.3, morphologically similar to G. lucidum, had the highest, followed by G. weberianum. Isolates of G. adspersum, G. applanatum from Europe and G. australe from Australia differed at most loci, thus the commonly accepted synonymy between G. australe and G. adspersum was not supported. Pectic isozymes alone were sufficient to distinguish three laccate (possessing a cutis surface consisting of a palisade of inflated hyphal ends) Australian species, G. weberianum, Ganoderma sp. Group 6.3 and G. cupreum, but they did not distinguish between the non-laccate G. australe and G. incrassatum. The laccate group contains species of greatest economic importance. Australian species were resolved by a single isozyme (glucose-6-phosphate dehydrogenase) using CAGE, demonstrating the potential for this method as a rapid diagnostic tool for identifying species of Ganoderma. This is the first reported population genetics based study of Ganoderma using isozymes.