The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA was amplified, cloned and sequenced from spores of five isolates of the arbuscular mycorrhizal fungus Glomus mosseae and one isolate each of G. fasciculatum, G. dimorphicum and G. coronatum. The sequences comprised ITSI (113–121 base pairs), 5.8S rRNA gene (154 base pairs) and ITS2 (222–230 base pairs). The ITS sequences were at least 84% identical, but only distantly related to other published sequences. Their identification as Glomus sequences was confirmed by sequencing part of the adjoining SSU rRNA gene from one isolate; it was 98% identical to the published G. mosseae sequence. Two to four clones were sequenced from each isolate, and in many instances these were substantially different (up to 6 % divergence) even when they were obtained from a single spore. Sequences from a single isolate were generally, but not always, more similar to each other than to those from different isolates. In addition to base substitutions, many ITS sequences differed slightly in length because of the insertion or deletion of up to three nucleotides within short runs of a single base, generally A or T. These changes were found at 22 separate sites within the ITS, and were more common between than within isolates. Phylogenetic relationships deduced from length variation and from base substitution were similar. The variation among isolates from different continents (Europe, Asia, South America) was no greater than among those from a smaller geographic range. The ITS1 and 2 sequences from G. caronatum were clearly distinct from the other isolates (11–16% divergence), but those of G. fasciculatum and G. dimorphicum fell within the range of variation exhibited by G. mosseae.