Human-induced biodiversity decline has been on the rise for the past 250 years, due to various causes. What is equally troubling, is that we are unaware which plants are threatened and where they occur. Thus, we are far from reaching Aichi Biodiversity Target 2, i.e., assessing the extinction risk of most species. To that end, based on an extensive occurrence dataset, we performed an extinction risk assessment according to the IUCN Criteria A and B for all the endemic plant taxa occurring in Greece, one of the most biodiverse countries in Europe, in a phylogenetically-informed framework and identified the areas needing conservation prioritization. Several of the Greek endemics are threatened with extinction and fourteen endemics need to be prioritized, as they are evolutionary distinct and globally endangered. Mt. Gramos is identified as the most important conservation hotspot in Greece. However, a significant portion of the identified conservation hotspots is not included in any designated Greek protected area, meaning that the Greek protected areas network might need to be at least partially redesigned. In the Anthropocene era, where climate and land-use change are projected to alter biodiversity patterns and may force many species to extinction, our assessment provides the baseline for future conservation research, ecosystem services maintenance, and might prove crucial for the timely, systematic and effective aversion of plant extinctions in Greece.