Turkey has an impressive richness in terms of fauna and flora. Nearly 28% of total country area of Turkey is covered by the forests. The aim of this research is to present the status, opportunities and challenges for forest biodiversity in Turkey according to EU Natura 2000 concept. This concept is a European ecological network which is occurred species and habitats designated by the EU Member States based on legally binding legislation. The importance of directives is emerging by designation of their special conservation areas under Natura 2000 sites. Designation of sites under those Directives takes some processes. SACs designed as sites to protect EU importance plants, animals and wildlife habitats which are assessed by the Habitats Directive. SPAs are sites of conservation value for rare and threatened European bird species which are designated under the Birds Directive. The species richness and habitat diversity of Turkey's forestry is a challenge for both Turkey and EU. Turkey includes species belonging to three different floristic regions. This opportunity is not common among EU countries. The forest types of Turkey have more structured importance according to diverse vulnerable species and biogeographically distribution of habitats than European countries. It should be thought that the number of Europe's forest habitat types could be considerably increase with Turkey's forest types. Before the selecting, designing and managing, the Natura 2000 sites in Turkey are needed some research to supply the assessment criteria for national assessment of species and habitats. The existing protected areas of Turkey and important endemic plant areas are available as potential Natura 2000 sites at national level. One of the most important deficiencies is lying in the inadequacy of data that will not supply some criteria to select and design the Special Areas for Conservation at European level.