In its report on the state of nature for the period 2007-2012, the EU describes the state of conservation of the species and habitat types protected by the Habitats and Birds Directives. As a result, forest habitats as a whole are not in a good conservation status and a lot still needs to be done if the goals of the Biodiversity Strategy and the new EU Forest Strategy are to be achieved by 2020. The following article presents the system of protection of Natura 2000 areas and discusses its consequences for the management of forest areas in Special Areas of Conservation and Special Protection Areas. In detail, it is about setting conservation goals, the avoidance of deterioration, checking the compatibility of projects, conservation measures, and management plans.