Verrucaria pakistanica is described as a novel species from District Kohistan, Khyber Pakhtunkhwa Province. It is characterised by thick, deeply areolate thallus, large superfcial perithecia, a thick involucrellum (80–105 µm), i.e., conical, not reaching the substratum and larger ascospores (20–29×7–10 µm) than the similar V. muralis. Phylogeny of ITS and nuLSU region confrms its position within the genus Verrucaria and morphological comparison makes it distinct from other related species of the genus. Keywords: ITS · LSU · Phylogeny · Taxonomy.