Persepolis, a UNESCO World Heritage Site in south-western Iran, dates back to more than 2500 years ago, and is colonized by a great diversity of lichen-forming fungi. A survey of the lichen-forming fungi revealed a species abundant in different areas of the cultural site, which turned out to be a new species of the genus Circinaria. The new species, Circinaria persepolitana, is introduced and described on the basis of morphological and molecular data. Circinaria persepolitana is characterized by having a crustose thallus, rimose to areolate, usually with bullate areoles, with an olive green to olive-brown surface and angular to elongate areoles in the marginal zone. Phylogenetic analyses including other species of the genus showed that the new species is phylogenetically close to C. mansourii, C. ochracea and C. reptans. We propose a new combination of Circinaria reptans (Looman) Sohrabi, Owe-Larsson & Paukov. The bioweathering capacity of the new species was also analyzed by scanning electron microscopy, examining the interface between the lichen thallus and the lithic substratum to assess its potential threat to the conservation of heritage surfaces. We found this species to be a potential biodeteriogenic agent, as thalli were closely attached to the lithic substratum and biogeophysical and biogeochemical changes at the rock surface could be associated with the colonization.