Biodiversity is seen as a core-service of marine ecosystems, and rare and endangered species play a crucial role in maintaining biodiversity. In shallow shelf seas such as the North Sea, benthic organisms contribute significantly to overall biodiversity. Hence, knowledge of biological characteristics and spatial distribution of benthic biodiversity and of benthic rare species is essential for sustainable ecosystem management and for the conservation of endangered species. In 2013, the status of endangered species was revised and published via the new “red list”. Regarding the marine benthic species on this list, the evidence used to judge them “endangered” is quite often scientifically unsatisfying by insufficient data and an imperfectly picture on their spatial occurrence. We use an extensive information system on benthic invertebrates in the German EEZ of the North Sea (>9000 stations x >740 species) for a high-resolution and large-scale analysis of occurrence and spatial distribution of “red list” species. For the first time, we evaluate the functional role of endangered species by means of their biological traits and analyse their spatial distribution in the EEZ. Finally, we identify potentially sensitive areas where endangered species cluster. This information constitutes a sound scientific base for a sustainable ecosystem management.