We analysed ketoacyl synthase domains of type I polyketide synthase (PKS) gene fragments of 163 lichenized and 51 non-lichenized fungi in a Bayesian phylogenetic framework. Lichenized taxa from several unrelated taxonomic groups, some of which produce identical secondary metabolites, were included. We found 12 clades of non-reducing PKS genes, which represent monophyletic PKS paralogues. PAML and SELECTON analyses indicated that purifying selection is the prevailing selective force in the evolution of the keto synthase domain of these paralogues. We detected no unambiguous correlation between PKS clades and the distribution of lichen substances. Together with the strong evidence for purifying selection, the wide distribution of certain paralogues in ascomycetes suggested early gene duplication events in the evolutionary history of this gene family in the Ascomycota.