The goal of ecosystem-based marine spatial management is to maintain marine ecosystems in a healthy, productive and resilient condition; hence, they can sustainably provide the needed goods and services for human welfare. However, the increasing pressures upon the marine realm threaten marine ecosystems, especially seabed biotopes, and thus a well-planned approach of managing use of marine space is essential to achieve sustainability. The relative value of seabed biotopes, evaluated on the basis of goods and services, is an important starting point for the spatial management of marine areas. Herein, 56 types of European seabed biotopes and their related goods, services, sensitivity issues, and conservation status were compiled, the latter referring to management and protection tools which currently apply for these biotopes at European or international level. Fishing activities, especially by benthic trawls, and marine pollution are the main threats to European seabed biotopes. Increased seawater turbidity, dredged sediment disposal, coastal constructions, biological invasions, mining, extraction of raw materials, shipping-related activities, tourism, hydrocarbon exploration, and even some practices of scientific research, also exert substantial pressure. Although some first steps have been taken to protect the European sea beds through international agreements and European and national legislation, a finer scale of classification and assessment of marine biotopes is considered crucial in shaping sound priorities and management guidelines towards the effective conservation and sustainability of European marine resources.