ITS, group I intron and partial β-tubulin sequences were used to infer phylogenies of a putative lichen species pair: Physcia aipolia (sexual) and P. caesia (asexual). A jackknife tree obtained from the β-tubulin sequences produced a well-resolved tree, whereas the resolution in the group I intron and in the ITS tree was lower due to homoplasy. The results obtained from the combined group I intron, ITS and β-tubulin data indicate that neither P. caesia nor P. aipolia are monophyletic and suggest that the two taxa are conspecific. Although the combined DNA data suggest the existence of several genetically isolated lineages in the P. aipolia/caesia group, the different lineages were not correlated with any morphological characters. Within one of the lineages, the incongruent placement of one P. aipolia specimen may indicate sexual recombination. A contradictory placement of one P. caesia specimen in different trees suggests that the usually asexual P. caesia is occasionally capable of sexual reproduction. The β-tubulin gene was found to contain enough variation for inferring relationships at the species level. Most of the informative characters were found from intron sequences and third codon positions in the exon regions. All the nucleotide substitutions were synonymous. Key Words: Ascomycetes, cryptic species, evolution, genetic marker, Lecanorales, lichenized fungi, parsimony jackknifer.