Three new species Lobothallia elobulata, L. iqbalii, and L. pakistanica from Pakistan are described as new to science and illustrated. Lobothallia elobulata is characterized by the absence of lobes, the presence of a distinct black hypothallus, and small, almost sphaeric ascospores 9–12 × 5–8 μm. Lobothallia iqbalii is characterized by its crustose–placodioid thallus with large appressed apothecia, single on areole, a high hymenium, 100–150 μm tall, and absence of prothallus and secondary metabolites. Lobothallia pakistanica is characterized by its thin, closely adnate, lobate thallus, lecanorine–aspiciloid apothecia, 2–3 on areole, and the absence of secondary metabolites. A comparative morpho-anatomical study and ITS-based molecular analysis confirmed the position of the species within the genus Lobothallia. Keywords Gilgit–Baltistan . Azad Jammu and Kashmir . Kohistan . Lichenized fungi . Taxonomy . ITS . Phylogeny.