Anthropogenic climate and land-use change pose major threats to island floras worldwide, yet few studies integrate these drivers in a single vulnerability assessment. Here, we examine the endemic flora of Evvia, the second largest Aegean island in Greece and an important biodiversity hotspot, as a model system to address how these disturbances may reshape biodiversity patterns. We used species distribution models integrating climate projections and dynamic land-use data to forecast potential range shifts, habitat fragmentation, and biodiversity patterns for 74 endemic taxa through 2100. Our findings reveal pronounced projected range contractions and increased habitat fragmentation for all studied taxa, with more severe impacts on single-island endemics. Current biodiversity hotspots, primarily located in mountainous regions, are expected to shift towards lowland areas, probably becoming extinction hotspots. Emerging hotspot analysis identified new biodiversity centres in lowland zones, while high-altitude areas showed sporadic hotspot patterns. Temporal beta diversity analysis indicated higher species turnover of distantly related taxa at higher elevations, with closely related species clustering at lower altitudes. This pattern suggests a homogenisation of plant communities in lowland areas. Assessment of protected area effectiveness revealed that while 94.6% of current biodiversity hotspots are within protected zones, this coverage is projected to decline by 2100. Our analysis identified conservation gaps, highlighting areas requiring urgent protection to preserve future biodiversity. Our study reveals valuable information regarding the vulnerability of island endemic floras to global change, offering a framework applicable to other insular systems. Our findings demonstrate that adaptive conservation strategies should account for projected biodiversity shifts and serve as a warning for other insular biodiversity hotspots, urging immediate actions to maintain the unique evolutionary heritage of islands

Recent research in island biogeography has highlighted the important role of late Quaternary sea-level fluctuations in shaping biogeographical patterns in insular systems, but largely focused on volcanic oceanic systems. Through this study we aim to extend this work by investigating the role of late Quaternary sea-level fluctuations in shaping species richness patterns in continental shelf island systems. Focusing on the Aegean archipelago, we first reconstructed the area’s geography using published data, under three sea-level stands: 1) current; 2) median over the last nine Glacial-Interglacial cycles; 3) Late Glacial Maximum (LGM). We compiled taxon-island occupancy for angiosperms (70 islands) and centipedes (56 islands). We investigated the impact of present-day and past geographical settings on chorological groups by analysing Island Species-Area Relationships (ISARs) and using Generalized Linear Mixed Models selection based on multiple metrics of goodness-of-fit. Our results confirm that the Aegean’s geography has changed dramatically since the LGM, while the median sea-level scenario only modestly differs from the present configuration. Paleogeographical changes largely shaped Aegean plant diversity patterns, and to a lesser degree centipede species richness patterns. The LGM geographic configuration affected both native and endemic species diversity through establishing connections between land-bridge islands and the mainland. Particularly on land-bridge islands we detected supersaturation of native species and stronger underrepresentation of endemics on those same islands. Unlike oceanic islands, where the longer lasting median configuration has ample effect on the current species diversity, the shorter lasting LGM configurations promoted increased connectivity with the mainland counteracting processes promoting endemism. Our study shows that in terms of processes affecting species richness patterns, continental archipelagos differ fundamentally from oceanic systems, highlighting the importance of distinguishing between them while studying biota from the perspective of historical biogeography.