Phylogeny inferred from ITS DNA sequence resolved isolates of Australian Ganoderma into five terminal clades. The phylogenetic analysis was considered superior to sequence variation statistics for delineating species as intra and inter-specific variation were dissimilar across the taxa studied. The analysis also revealed that a number of isolates had been misnamed. Phylogeny inferred from the sequence data supported the retention of Elfvingia and Ganoderma as subgenera of Ganoderma, and the placement of the G. chalceum complex within subgenus Ganoderma. These findings were, however, poorly supported by decay analysis. G. adspersum, a European species considered to be a synonym of G. australe (a species which is in need of neotypification) by some authors, was not synonymous with G. australe from Australia. G. incrassatum from Northern Australia formed a clade with isolates named G. gibbosum from China and an isolate named G. australe from Taiwan. G. weberianum from Australia, originally identified by R. L. Steyaert, formed a terminal clade that was closely related to a second terminal clade comprised of two G. weberianum isolates and an isolate of G. microsporum from Asia. It was concluded that the clades represented two allopatric populations of G. weberianum and that G. microsporum was a synonym of G. weberianum. Isolates determined as G. chalceum by R. L. Steyaert and referred to here as G. cupreum formed a distinct terminal clade most closely related to material identified as G. sinense. A species mistaken for G. lucidum from Australia and Indonesia, a species from temperate and South East Asia containing commercially cultivated strains, and an Argentinean species showed evidence of allopatric speciation. Nomenclatural problems and the implications of our study on the pharmaceutical and commercial exploitation of Ganoderma in Australia are discussed.