Abstract Given the continuous loss of biodiversity, there is an urgent need to study its patterns to generate conservation measures. Complementing traditional biodiversity measures with indices that incorporate evolutionary aspects such as phylogenetic diversity or phylogenetic endemism (PD or PE) allows us to infer possible historical processes that could explain the conformation of current biodiversity. In this study, patterns of richness and endemism were determined and contrasted with the evolutionary indices PD, PE, PDres (residual PD), RPD (relative PD) and RPE (relative PE) for the woody flora in a latitudinal gradient (30°S to 40°S) in the Chilean coastal range. A phylogenetic tree was constructed using three DNA regions to calculate evolutionary indices (PD and PE) and compare them at different taxonomic levels. The results of PD and PE were spatially consistent with those of richness and endemism, but evolutionarily important sites were discovered. PD-derived indices indicate three evolutionary hotspots: a cradle-type site with a predominance of neoendemics (generating recent diversity) at 33°S, three museum-type sites with a predominance of palaeoendemics (maintaining relict diversity) at 30°S, 38°S and 40°S and one with high PD and PE at 37°S. We found evolutionary hotspots within the hotspot of Central Chile with different characteristics. Incorporating measures that consider the evolutionary aspect has important implications for the conservation of highly diverse and endemic areas.