Naxos and Amorgos are islands in the Aegean Sea with a typically arid to semiarid climate, the vegetation being dominated by thermo-Mediterranean shrubs. From the floristic point of view, both are among the most interesting islands of the Cyclades. However, no data were available on their fungal diversity. This work presents an annotated check-list of the basidiomycetes belonging to the subclass Agaricomycetidae (Agaricales and Boletales) from these two islands. A total of 142 species and subspecific taxa are recognized and assigned to 58 genera. The genus Simocybe as well as 21 taxa at the species or subspecies level constitute new records for Greece, while further 76 taxa represent first national reports for habitat, hosts and/or substrates. A brief description of key diagnostic characters — in conjunction with a discussion of pertinent literature — is provided for the most interesting findings.