Considered as a hotspot for biodiversity in the Mediterranean Basin, Lebanon is currently witnessing anarchic urbanization and unprecedented destruction of its natural habitats. Unregulated urbanization is also compounded by the surge in Lebanon's population due to the unabated influx of Syrian refugees since 2012. This work aims to define Important Plant Areas (IPAs) with exceptional botanical richness. These IPAs should constitute the priority zones for conservation, contributing to the fulfillment of national targets in the framework of the Aichi Biodiversity Targets. A customised methodology was developed to suit to the Lebanese geomorphological characteristics, using an approach that combined three indicators: species richness; species conservation value including endemism and rarity; and, the habitat conservation value. Out of the characterized 1250 cells of 3 km × 3 km covering Lebanon, 11 were ranked as IPAs of very high importance and 20 as IPAs of high importance. These 31 top ranked cells covered 3% of Lebanon's area. These IPAs contained diverse habitat mosaics, including forests, mountain screes, cliffs and grasslands and host a total of 2386 species amounting to 79% of the flora of Lebanon and 80% of the species endemic to Lebanon. Seven of these top ranked cells contained species strictly endemic to Lebanon. Only 26% of these IPAs were already designated as protected areas and hosted 45% of Lebanon's plant species. This map of IPAs provides important information for stakeholders, practitioners and politicians involved in conservation in Lebanon to protect endangered zones and develop rational strategies for their conservation.