The Aegean archipelago, comprising numerous islands and islets with great heterogeneity in topographic, geological, historical and environmental properties, offers an ideal natural laboratory for ecological and evolutionary research, and has been the stage for a very long interaction between human civilizations and local ecosystems. This work presents insights that have been gained from past and current relevant research in the area, highlighting also the importance of the Aegean archipelago as a useful model to address many major questions in biogeography, ecology and evolutionary processes. Among the most interesting findings from such studies concern the role of habitat heterogeneity as the most important determinant of species richness, the development of a new model (Choros) for the species–area–habitats relationship, the mechanistic aspects of the Small Island Effect, the very high rates of species turnover, the lack of a role for interspecific competition in shaping species co-occurrence patterns in most cases, the importance of non adaptive radiation in diversification of several taxa, the insights into the relative roles of vicariance and dispersal in speciation, the understanding of the interplay between human presence and the establishment of exotic species and extinction of indigenous biotas. Concluding, the Aegean archipelago is an ideal stage for research in evolution, ecology and biogeography, and has the potential to become a model study area at a global level, especially for land-bridge, continental islands.