Aiming to cope with the provisions of Aichi Biodiversity Targets, EU Biodiversity Strategy and EU Green Deal, we conducted the first nationwide, phylogenetically informed identification of vascular plant diversity hotspots and endemism centres in Greece. By this, we identified the most important factors that shaped them, and assessed the effectiveness of the Special Areas of Conservation of the Natura 2000 network in safeguarding them. Qualitative and quantitative results are provided and presented in thematic maps and relevant diagrams, highlighting areas of conservation importance, and identifying current protection scheme gaps. Simultaneously, our work contributes to national efforts for drafting Natura 2000 sites Management Plans, as well as to the MAES implementation in Greece.Biodiversity hotspots (BH) cover a small fraction of the Earth’s surface, yet host numerous endemics. Human-induced biodiversity loss has been increasing worldwide, despite attempts to halt the extinction crisis. There is thus an urgent need to efficiently allocate the available conservation funds in an optimised conservation prioritization scheme. Identifying BH and endemism centres (EC) is therefore a valuable tool in conservation prioritization and planning. Even though Greece is one of the most plant species-rich European countries, few studies have dealt with the identification of BH or EC and none has ever incorporated phylogenetic information or extended to the national scale. Consequently, we are unaware of the extent that Special Areas of Conservation (SAC) of the Natura 2000 network …