The importance of Natura 2000 network for the conservation of natural habitats, wild flora and fauna at European level is undeniable. However, it may not have reached its full potential since the loss of biodiversity continues to increase year on year. Further on, a third of the plant species listed in the Habitats Directive to guide the declaration of European Union Natura 2000 network of protected areas is not threatened and there is broad agreement on the need to review and update the species list. Here, the effectiveness of Natura 2000 in the conservation of Spanish bryophytes and vascular plants included in the Habitats Directive Annex II is analysed and compared with the one offered to the species included in the Spanish Red Lists. Results show a remarkable coverage of Natura 2000 over the distribution areas of threatened species, thus providing an umbrella effect on these taxa. It confirms that the number of plant species in the Habitats Directive could be significantly extended without altering the current configuration of the network. This would allow the incorporation of scientific advances produced since the Habitats Directive was approved almost 30 years ago, and will contribute to the goals of the new European Biodiversity Strategy for 2030, such as to consider impacts caused by alien species, land use or climate changes.