Taxonomic diversity is the most widely used indicator for biodiversity conservation although genetic and functional diversity are major drivers of biodiversity spatial and temporal structure. Within the fast-growing field of ecophylogenetics, we propose to test the congruence between taxonomic, phylogenetic, functional and paleoecological diversity of the tree species in the European Mediterranean region, in order to identify the factors underlying their spatial patterns. Our results will help prioritize biodiversity conservation measures using the poorly explored functional and evolutionary components of biodiversity. Ecophylogenetic and palaeoecological data for all native woody species of the study area will be collected. Spatial and meta-analyses and numerical modeling tools will be used to identify trends in patterns and level of congruence of three components of biodiversity. and to identify underlying driving factors. Our particular approach aims at combining contemporary explanatory variables with (i) paleoecological data, providing a proxy for past diversity and human influences, as well as (ii) data from phylogeography of tree species and community phylogenetic. This work will permit to evaluate current practices and develop recommendations for efficient conservation strategies.