Aim: The processes driving the assembly of the Central Aegean island communities remain unclear, even though the factors shaping the plant species richness patterns in the Cyclades are well known. In order to shed light on these processes, we identified biogeographical modules within the phytogeographical area of the Cyclades. Location: The Cyclades, Greece. Methods: We used a network approach to detect island biogeographical roles and modules, based on a large and detailed database including the Greek endemic plant taxa of the Cyclades and we tested for nestedness in the island-species matrices. Results: The Cyclades were significantly modular and divided into five biogeographical modules. Three of the modules were significantly nested and two displayed all four possible biogeographical roles (connectors, module hubs, network hubs, peripherals). Most of the network’s taxa are classified as peripherals and widespread endemics. Main conclusions: The five modules’ borders correspond remarkably well to the palaeogeographical and climatic compartmentalization of the Cyclades. The flora of the Cyclades has not yet reached the relaxation phase and the region may act as an ecogeographical filter for the distribution of several plant lineages. Naxos, Milos and Anafi play an important role for the network’s connectivity, while at least five adjacent phytogeographical regions affect the distribution patterns of the endemic taxa present in the Cyclades.