Mediterranean Chile is part of the five recognized mediterranean‐type climates in the world and harbours a very rich floral diversity. Climate change has been reported as a significant threat to its biodiversity. We used the flora of Mediterranean Chile to analyse how biodiversity patterns, as measured by phylogenetic diversity, genus and species richness will respond to climate change scenarios and identify the areas that will harbour the greatest evolutionary potential and biodiversity richness. We also evaluated how these spatial patterns are depicted within the current network of protected areas.