Isolates of Endothia eugeniae, a pathogen of clove (Syzygium aromaticum), and Cryphonectria cubensis, a pathogen of eucalyptus (Eucalyptus spp.), were examined with chemotaxonomic techniques, including thin-layer chromatography of fungal pigments and isozyme analysis. The bisanthraquinone pigments skyrin and oxyskyrin were isolated from mycelial extracts of each species. Isolates of E. eugeniae and C. cubensis could not be differentiated by polyacrylamide gel electrophoresis of buffersoluble proteins. The organisms also shared alleles at 16 presumed genetic loci, as detected by isozyme analysis. This study confirms the conspecificity of E. eugeniae and C. cubensis.