The new genus of lichenicolous fungi Austrostigmidium is described from Antarctica and Tierra del Fuego (Chile). It is characterized by the presence of black pseudothecia, pseudoparaphyses, fissitunicate, I−, KI− asci and 3-septate hyaline ascospores. So far, the only known species grows on Mastodia tessellata (Verrucariales, Eurotiomycetes). The new genus is compared with anatomically close genera. Based on nuLSU and nuSSU markers we inferred its phylogenetic relationships and found that it belongs to the family Teratosphaeriaceae (Capnodiales, Dothideomycetes) and is closely related to rock-inhabiting fungal species, as well as to the hyphomycetous lichenicolous fungus Xanthoriicola. Finally, the host-parasite interface has been analyzed by means of transmission electron microscopy and fluorescence microscopy in order to describe the interactions among the new fungus and the symbionts forming the host lichen.