An exploration in the Nomos of Dodecanisos, SE Aegean, Greece, mainly on the islands Kalimnos and Kos, and to a lesser extent on Telendos and Nisiros, revealed the presence of 290 lichen species. Of these, 12 were not recorded before from Greece, and four are described as new to science: Acarospora pseudofuscata, Buellia epifimbriata, Caloplaca aegaea and Pertusaria pseudoparotica. An annotated catalogue is presented, which includes notes on lichen records from Santorini and Paros. The lichen flora does not show any special affinity with the nearby Turkish mainland, in striking contrast to the phanerogam flora. It is similar to that of the Paros archipelago (Central Aegean Islands) and differences can be explained by different substrate availability and chance dispersal (island effect). The lichen flora of Santorini, a vulcanic island recolonized 3500 years ago, differs by a larger representation of widespread species. 15 species appear to have a restricted, eastern distribution in the Mediterranean.