The paper deals with the species diversity of aphyllophoroid fungi of the Valaam Archipelago (Lake Ladoga) and the Solovetsky Archipelago (White Sea). Survey findings amounted to 156 species in the Valaam Archipelago, and to 247 species in the Solovki. Approximate species diversity for the two territories can be estimated at 230–240 and 300–310 species, respectively. The two archipelagos had 117 species in common; and 19 species were recorded from insular areas only. The Sorensen–Czekanowsky distance between the areas is 0.58. Ecological analysis of the biodiversity showed that mesophilic species dominate in both areas, but the Valaam mycobiota features a higher share of xerophyles. Geographic analysis demonstrated the prevalence of multiregional and Holarctic species widely distributed through several (including boreal) zones. In the trophic aspect, the prevailing group is saprotrophs. The role of facultative species pathogenic for spruce, aspen and birch is higher than in the corresponding mainland areas. There are 28 epigeous species, 10 species are associated with old polypore fruit bodies, and 1 species was found on pine cones. The rare and vulnerable species list contains 35 items. It is demonstrated that insular ecosystems are significant reservoirs of fungal biodiversity. Some peculiarities of insular ecosystems in comparison to the mainland were revealed, as well as anthropogenic changes in the composition of rare and indicator species of aphyllophoroid fungi.