Genomic phage libraries of arbuscular mycorrhizal fungi were constructed for the first time, and clones containing ribosomal RNA (rRNA) genes isolated for Glomus mosseae and Scutellospora castanea. The number of rDNA clones per library indicates that these libraries can be also used to isolate genes with low copy numbers. Sequences of the 18S rRNA gene, of the internal transcribed spacer and of the 5.8S rRNA gene were analysed and compared. Differences between the 18S and the 5.8S rRNA genes were few and in the range of variation found for other fungi. In contrast, the internal transcribed spacers of G. mosseae and S. castanea were highly variable, showing the potential of this region for the identification of different species or isolates. Interestingly, nucleotide exchanges were found in this region when the sequence for G. mosseae was compared to those of two other clones of the same isolate.