Rimularia insularis forms an photosynthetic thallus on lichens of the Lecanora rupicola group. In the thalli of R. insularis, some hyphae of the host are detectable, and they are situated mainly in the basal part of the Rimularia's medulla. No Lecanora hyphae were present in the Rimularia's algal layer and they were indistinct in the upper parts of its medulla, from where we obtained clean ITS-sequences of Rimularia. Direct PCR from various sections of the algal layer detected only one photobiont genotype, although the algal cells could be assigned to two morphologically different types. Calcium deposits were found in the upper parts of the medulla, while abundant rock substrate fragments with different mineral compositions were present in the lower parts. Cavities and fissures in the rock below the infected thalli were filled by fungal cells, PCR analyses of such parts indicated that the Rimularia hyphae extend below the host, and into the rock.