The concept of species and species complexes of lichenized fungi is reviewed in the light of recent molecular approaches. Species concepts based on chemistry, morphology, reproductive mode, photobiont choice and habitat preference provide working hypotheses from which the delimitation of species or relationships within species complexes can be tested with molecular data. In studies in which a single locus such as ITS is used, a phylogenetic species concept can be applied only when the sequence data delimits genetically discrete clades that correlate with phenotypic characters or biogeographical distribution. This will be the case when sufficient time has passed for genetic isolation to result in the coalescence of different character states among the sibling species of a complex. In the case of recently diverged species, a single locus may not accurately separate species, and is not sufficient evidence to reject putative species based on a phenotypic species concept. In such cases, several genetic loci must be used to delimit species by a phylogenetic species concept. These phylogenetic species may corroborate phenotypic characters or biogeography, or they may be cryptic for all observed characters. Molecular analyses at the species level will lead to the re-evaluation of phenotypic characters for species delimitation, and will improve the understanding of speciation in lichenized fungi. The results from new molecular approaches have implications for taxonomic revisions. Formal changes in nomenclature based solely on molecular evidence should be made conservatively, and only after studies based on a thorough sampling with sufficient data of all kinds is performed, and after the taxonomic history of the group has been reviewed. In the meantime, informal names to describe new phylogenetic hypotheses are sufficient. Formally named cryptic species cause problems in distributional studies, where old material and literature references are included, but are useful in high resolution studies such as ecophysiology, especially where phenotypic differences may exist among cryptic species.