Since 2004 Germany established ten Marine Protected Areas (MPAs) in the German Economic Exclusive Zone (EEZ, 12-200 nautical miles zone) of the North and Baltic Sea as a contribution to the European Natura 2000 network. The main target of the coherent network of Natura 2000 sites is to reach a favourable conservation status of habitats and species. Even though commercial fisheries is known as one of those human activities in the marine ecosystem with the most severe negative impacts on habitats and species, fishing activities in the designated Natura 2000 sites are almost unregulated up to now. To analyze the impacts of fisheries on habitats and species in Natura 2000 sites and to develop site specific management plans the Federal Agency for Nature Conservation (BfN) had initiated in 2006 the research and development project “Environmentally Sound Fisheries Management in Marine Protected Areas” (EMPAS), which was accomplished by the International Council for the Exploration of the Seas (ICES). EMPAS was a pioneering approach in Europe, which benefited by the participation of different scientist from marine and fisheries biology, as well as stakeholders from the fishing industry and nature conservation. This book gives a comprehensive overview of the process and the results of the EMPAS project as well as the scientific advice for management measure in marine Natura 2000 sites given by ICES. A further chapter presents presentations given at the international conference “Marine Natura 2000 sites and Fisheries management: The results of the EMPAS project” November 2008 in Stralsund.