The lists include several hundred species of plants and animals. They do not include any fungi, lichens or birds.
European Union states are required under the Habitats Directive to protect the listed species, and for some species (those listed in Annexe II), they are required to designate Special Areas of Conservation (SACs) to protect populations of them.
These regulations help to protect areas of land from development which will harm or destroy those species... without this protection developers will be free to ride roughshod over any land irrespective of what it contains.