To delineate the biogeographic structure of Lebanon based on native tree and shrub species distribution using ecological niche modeling and dissimilarity indices. Lebanon, Middle East, and Mediterranean basin (34° N-35° W). We compiled a species list of Lebanon phanerophytes and used ecological niche models (ENM) to obtain surface distributions for each species. Then we defined groups of species with overlapping whole distributional ranges (global chorotypes) and significantly similar distributions within Lebanon (regional chorotype). To evaluate spatially grouped sets of species, we mapped the predicted distribution of species belonging to each chorotype. We measured the biogeographic distinctness amongst them using turnover and nestedness indices. Finally, we identified biogeographic transition zones based on the geographical mixture of chorotypes within Lebanon. We grouped the 60 species into nine global and five regional chorotypes. The chorotypes encompassing more than half of all species were rather nested and occurred on the western side of the country at low to middle elevations of Mount Lebanon (Mediterranean and Euro-Siberian chorotypes). The most dissimilar chorotypes occurred in the northeastern part of the country on the Anti-Lebanon mountains (Irano-Turanian) and the southern lowland (Saharo-Arabian). We found a hotspot of species richness at intermediate elevation on the northwestern slopes of the Lebanon range and a biogeographic transition zone at high elevation and the eastern slopes of Mount Lebanon, as well as the southern Anti-Lebanon mountains. Species distribution models allowed us to overcome gaps in occurrence data when studying biogeographical delineation. The first biogeographical structure of Lebanon was generated. The western part of Lebanon belongs to the (East) Mediterranean region, and the northeastern part to the Irano-Turanian region. The remaining areas are part of biogeographical transitional zones. The few endemic trees are characteristics of these transition zones.