Little information currently exists on species diversity in communities of arbuscular mycorrhizal fungi (AMF), mainly owing to difficulties in identification of field extracted spores on the basis of morphology. The possibility was explored to identify individual AMF spores from the field on the basis of a molecular marker, namely the nuclear ribosomal DNA encoding the highly conserved 5.8S rRNA with the two flanking internal transcribed spacers (ITS region), known to vary between species. A technique involving polymerase chain reaction followed by restriction fragment length polymorphism analysis (PCR–RFLP) was developed to amplify and characterize the ITS region from single AMF spores. PCR reactions with extracts from single spores of three AMF species, raised under glasshouse conditions, yielded reproducibly a single amplification product of the ITS region in sufficient amounts to allow cleavage with several restriction enzymes. The size of the ITS region, c. 600 base pairs, varied only slightly between species. Digestion of the PCR products with the restriction enzymes Hinfl and Taq I resulted in banding patterns that were reproducible for different individual spores of a given species, but showed clear differences between the three species tested. The sum of the fragment sizes was sometimes greater than the size of the original PCR product, e.g. in Glomus mosseae. Clones of the amplification product from a single spore of this fungus were obtained and sequenced. This yielded two closely related but different sequences, indicating that two different ITS regions co-existed in the spore. The RLFP pattern of the amplification product of the spore was a result of an amalgamation of these two sequences. The technique was applied to AMF spores collected from a species-rich grassland. Spores were sorted into morphological groups on the basis of their colour, size, and shape, and then subjected to PCR–RFLP analysis. In some morphological groups, a large percentage of spores failed to yield an amplification product, probably because they had lost their contents. A group of Glomus spores yielding amplification products in the majority of cases was further investigated: PCR RFLP analysis on 10 individual spores from the field produced 10 different patterns. Similar results were obtained with other groups of spores. The results suggest that the diversity in natural AMF communities and the genetic diversity within individual spores might he much greater than previously thought.