Aim The Aegean Archipelago has been the focal research area for identifying and testing several ecological and evolutionary patterns, yet its biogeographical subdivision has been somewhat overlooked, with the processes driving the assembly of the Aegean island plant communities still remaining largely unclear. To bridge this gap, we identify the biogeographical modules (highly linked subgroups of islands and plant taxa) within the Aegean Archipelago. Location The Aegean Archipelago, Greece. Methods We used a network approach to detect island biogeographical roles and modules, based on a large and detailed database including 1498 Aegean endemic and subendemic plant taxa distributed on 59 Aegean Islands and five adjacent mainland areas. Results The Aegean was divided into six biogeographical modules; the network was significantly modular. None of the modules displayed all four possible biogeographical roles (connectors, module hubs, network hubs, peripherals). Six new biogeographical regions in the Aegean were identified. Main conclusions The borders of the six biogeographical regions in the Aegean correspond well to the region’s palaeogeographical evolution from the middle Miocene to the end of the Pleistocene. The Central Aegean acts as an ecogeographical filter for the distribution of several plant lineages across the Aegean Sea, while there seems to be a N–S-oriented biogeographical barrier in the Aegean corresponding to the palaeogeographical situation during the middle Ionian. These biogeographical barriers have been fundamental for both plants and animals.