A lichen inventory on the Aegean islands of Paros and Antiparos, both with a long history of land vegetation and a wide variation in bedrock, revealed the presence of 268 species. This flora is compared with the 182 species known from the nearby Santorini island group, comparable in size and surface morphology, but a volcanic archipelago with few limestone inclusions, which was completely devastated by an eruption about 3000 years ago. The higher species number of Paros is explainable by the difference in size and substrate availability. Lichen species inhabiting siliceous-crystalline rock and epiphytic lichen species are more strongly represented on Paros, while species of volcanic rock are more numerous on Santorini, in accordance with the frequency of these substrates. There is no evidence for an influence of the uninterrupted history of the plant cover of Paros on the α-diversity of its lichen flora. Differences in species composition other than those depending on substrate availability appear to be of a random type. Vegetative reproduction seems slightly less frequent on Paros, and pioneer species of lava, which, on Santorini, are restricted to young lava fields, are absent from Paros. An annotated list of lichen species for Paros and an updated checklist for Santorini are presented. Among the encountered species, 28 appear to be unrecorded for Greece. All species reported from Paros are new for this island, from where no species were reported before. Pertusaria parotica is described as a species new to science and the new combination Protoparmelia psarophana var. reagens is made.