The molecular diversity of glomalean fungi was studied by analysis of Glomus specific sequences amplified from field harvested peas. Glomus specific, large rDNA sequences were amplified from roots in a nested PCR reaction, following primary amplification with eukaryote specific primers. The nested primers were designed to amplify a lineage within the genus Glomus including G. mosseae, G. caledonium and G. geosporum, all of which had repeatedly been isolated from trap cultures set up with soil from the field. Single-stranded conformation polymorphism (SSCP) was used to screen the nested PCR products for presence of multiple sequence types. Nested PCR products were sequenced if necessary after reamplification of single SSCP types. The root derived sequences were aligned with sequences from spores of 17 cultured Glomus isolates; five of these isolated from the same field from where the peas were harvested. Some of the root-derived sequences were from lineages other than those species isolated from the field and some of the isolated species were not retrieved as sequences from the roots.