Depside and depsidones are polyphenolic compounds with important ecological and pharmaceutical implications, but many details of their biosynthesis are still under investigation. We describe a molecular analysis of the two chemotypes of Pseudevernia furfuracea, one producing the depside olivetoric acid, and the other the corresponding depsidone physodic acid. Using genomics and transcriptomics, we detect a biosynthetic gene cluster putatively involved in olivetoric/physodic biosynthesis in Pseudevernia furfuracea. This cluster has similarity to a cluster in Cladonia grayi associated with the synthesis of the depside/depsidone pair 4-O-demethylsphaerophorin/grayanic acid. The putative P. furfuracea cluster contains a non-reducing polyketide synthase (NR-PKS) and a cytochrome p450 (cyt p450). This supports that the PKS synthesizes and joins both aromatic rings of the depside, and that cyt p450 converts the depside to the corresponding depsidone. This is the first study to identify the putative physodic and olivetoric acid gene cluster. We also propose a specific mechanism of depside synthesis by the PKS. Our study contributes to the understanding of natural product synthesis in lichenized fungi.