Lobothallia pulvinata is described and illustrated here from Pakistan. The species is characterized by a thin thallus, large lecanorine apothecial discs, (0.3–1.2 mm), smaller ascospores, (8–12×4–6 µm) and the presence of norstictic acid than the similar L. pakistanica. Both the morphological and molecular characters confrm the novelty of this taxon. The phylogenetic position within the relatively recent genus-level circumscription of the family Megasporaceae is confrmed based on nrITS and mtSSU sequence datasets. Description, phylogenetic analysis and a comparison table with other Lobothallia species are provided. A brief note on L. iqbalii, norstictic acid chemotype is also presented. Keywords: Chilas · Kohistan · Phylogeny · Taxonomy.