Benthic habitat condition assessments are a requirement under various environmental directives. The Marine Strategy Framework Directive (MSFD),for example, challenges member states in a European sea region to perform comparable assessments of good environmental status and improve coherence of their monitoring programmes by 2020. Currently, North Sea countries operate independent monitoring programmes using nationally defined assessment areas. Lack of an agreed OSPAR or EU scale monitoring method and programme has been identified as a priority science need. This paper proposes a method for the development of a coherent and efficient spatial sampling design for benthic habitats on regional level and gives advice on optimal monitoring effort to get more accurate assessments. We use ecologically relevant assessment areas (strata) across national borders and test spatial sample allocation methods.