The phylogeny of the genus Pertusaria and allied taxa was investigated using nucleotide sequences of the LSU rRNA gene. Sequences from these regions of 15 pertusarialean fungi were aligned to those of three representatives of Agyriales used as outgroup. The alignment was analysed cladistically using maximum parsimony. The Pertusariaceae appear paraphyletic bearing the monophyletic Coccotremataceae on a clade including Ochrolechia and Pertusaria subg. Monomuratae, but monophyly of the family cannot be rejected. The genus Pertusaria is polyphyletic, with the subgenus Monomuratae more closely related to the Coccotremataceae and Ochrolechia than to taxa of the subgenera Pertusaria and Pionospora. Monophyly of the genus Pertusaria is rejected. The monophyly of the subgenera Pertusaria and Pionospora is also rejected. The distribution of selected characters in the Pertusariales is investigated and it is shown that apothecial form and spore wall number have changed in parallel within Pertusaria. The Pertusaria-type ascus is plesiomorphic within the Pertusariaceae and thus cannot be used to circumscribe Pertusaria. The presence of chlorinated xanthones is restricted to Pertusaria s. str