The Habitats Directive 92/43/EEC wants to promote the maintenance of biodiversity, taking account of economic, social, cultural and regional requirements. It establishes the EU wide Natura 2000 ecological network of protected areas to assure the long-term survival of Europe's most valuable and threatened species and habitats. The network incorporates Special Areas of Conservation designated by Member States under the Habitats Directive and Special Protection Areas designated under the 1979 Birds Directive. A full implementation of the Habitats Directive implies that all enlisted habitats and species attain a favourable conservation status all over the European territory. The term favourable conservation status refers to the optimal and long-term ecological functioning and conservation of habitats and species. Each member state has to make its own interpretation, which is expected to be based on scientific insights. Most Habitat Directive areas encounter severe environmental bottlenecks. Desiccation, acidification and eutrophication occur very often. To reach a suitable conservation status of habitats a huge effort is needed in environmental restoration combined with ecological restoration techniques. Furthermore damaging activities that could significantly disturb these species or deteriorate the habitats of the protected species or habitat types should be avoided. Therefore an appropriate assessment -required under Article 6 of the habitats directive- can be made. In this talk we want to give attention to the contribution of scientific research in the assessment of the impact of a project or plan, either alone or in combination with other projects or plans, on the integrity of the Natura 2000 site, with respect to the site’s structure and function and its conservation objectives. The Flemish government (Northern Belgium) is now giving priority to vegetation science underpinning each stage in the step-wise approach of the assessment. This should result in more detailed habitat maps, clear habitat definitions, a ...