Invasion by non-native pines causes reduction and fragmentation of cork oak forests.
Pine stands negatively affected γ-, α- and β-plant diversity of cork oak areas.
Phylogenetic diversity, inferred from a ad-hoc nrDNA tree, declined in pine stands.
Over-dispersed phylogenetic structure of cork oak forests was lost in pine stands.
Active management of pine stands will help to recover diversity of cork oak areas.