The small‐island effect (SIE) describes a different relationship between island area and species richness on smaller compared to larger islands. The pattern has recently gained widespread support. However, few studies have attempted to identify the actual mechanisms driving the SIE. Here, we use a phylogenetic community framework to study the SIE, based on the assumption that if the dominant assembly processes differ between small and large islands, patterns of phylogenetic community structure should shift across the area and habitat diversity gradient.The Aegean Archipelago, Greece.Plants.We used a large dataset of 3,262 vascular plant species distributed across 173 islands, in combination with a species‐level phylogeny. The phylogenetic community structure of each island was calculated using a null modelling framework and was quantified using effect sizes (ES …