Small insertions are reported from the SSU rDNA of the genera Cladonia, Cladina, Stereocaulon, Pertusaria and Physcia (lichen-forming Lecanorales, Ascomycetes). The insertions range in length from 56 to 81 nucleotides, and occur at a shared position, 330 (relative to Escherichia coli), in a semi-conserved region of the SSU rDNA. These small insertions have a simple secondary structure with two stem-loops, and may represent degenerate group-I introns. Species of the same genus often have small insertions of similar lengths, secondary structures and sequences. These similarities suggest that the insertions are homologous and can provide phylogenetic information to support current classifications. Variable sequences of rDNA, such as the small insertions and group-I introns, may be powerful tools for resolving evolutionary relationships among genera and species.