The species in Lobaria sect. Lobaria are circumscribed based on secondary metabolites and the morphology of vegetative propagules such as isidia and soredia. Lobaria pulmonaria typically forms soredia, which distinguish it from the other species of this section. However, in L. pulmonaria soredia may develop into isidioid soredia that can be confused with isidia. In Macaronesia, this difficulty gave rise to controversial discussion about the taxonomic status of L. pulmonaria var. meridionalis, which forms cylindrical diaspores. In the present study, a three loci approach (ITS, RPB2 and EF-1α) was used to investigate the taxonomic status of L. pulmonaria var. meridionalis based on a phylogeny of Macaronesian taxa of the L. pulmonaria group. Phylogenetic analyses reveal that L. pulmonaria v. meridionalis is a distinct taxon, which is here proposed at the rank of species: Lobaria macaronesica Cornejo & Scheidegger sp. nov. The new species is genetically distinct from the Asian L. meridionalis, the cosmopolitan L. pulmonaria and the Macaronesian L. immixta.