This collaborative investigation was aimed at using morphological and molecular characters to study inter- and intraspecific variation within isolates of Glomus mosseae and Glomus coronatum from different parts of the world. A secondary aim was to assess whether any divergence found was genetically based and/or correlated with the biogeographic origin of isolates. Morphological evaluations of various possible taxonomic characters including spore colour, size, sporocarp architecture and hyphal attachment morphology, showed that only spore colour could discriminate the two groups. Isozyme analysis of malate dehydrogenase and esterase loci clearly confirmed this grouping of the two species complexes. SDS profiles and cluster analysis showed the same separation on a selection of isolates from the two groups. A comparison of a representative isolate from the G. coronatum group (BEG 49) with other arbuscular mycorrhizal fungi using G. mosseae-specific primers also provided evidence for separation of the two species complexes. The data and methodology employed provide a blueprint for future multimodal and multidisciplinary approaches to the unravelling of taxonomic problems within this ancient group of symbiotic fungi.