Pyrenidium is a lichenicolous genus which was included in the family Dacampiaceae (Pleosporales) based on morphological characters. The classification of this genus within Dacampiaceae has been controversial due to the lack of sequence data. In this study, the genus Pyrenidium is sequenced for the first time using five freshly collected specimens belonging to the generic type and two other species. Although the morphology of Pyrenidium is quite similar to other genera of Dacampiaceae, phylogenetic analyses from nuLSU and nuSSU sequence data demonstrate that Pyrenidium is distantly related to Dacampiaceae and it forms a distinct lineage within the Dothideomycetes. Therefore, we resurrect the family Pyrenidiaceae to accommodate Pyrenidium. Morphological descriptions of the sequenced specimens of Pyrenidium are provided and include the description of a new species, P. borbonicum.