The length of the small subunit ribosomal DNA (SSU rDNA) differs among isolates of species and varieties of Gaeumannomyces. The sequence of the 3' region of the SSU rDNA revealed 340-, 365-, and 520-bp insertions for G. graminis varieties avenae, tritici, and graminis, respectively. The intron sequences from varities tritici and avenae were similar, except there was an insert of 23 nucleotides at base 328 from the 5' end of the G. g. var. tritici intron. The G. g. var, graminis intron sequences had 92.4% homology compared with the intron sequences of varieties tritici and avenae. In addition, the intron sequence of variety graminis is larger, having an insert of 155 nucleotides at base 365 of the 5' end of the intron. Little variation in the DNA sequences flanking the introns has been detected among the isolates of Gaeumannomyces that either have or lack an intron. Reverse transcriptase PCR (RT-PCR) indicated the absence of the intron in the mature rRNA. The intron sequence had both a conserved sequence and secondary structural elements classifying it as a group I intron.