The present thesis focuses on the development and application of a biological tool that can be used as a decision support system for marine management. The main aim of the thesis was to develop a marine biological valuation methodology that is able to integrate all available biological information of an area into one indicator of intrinsic value. This methodology should be applicable in every marine environment, independent of the amount and quality of the available biological data and the habitat type, and should be acceptable by a wide scientific audience. The five main objectives of the thesis were: (1) to develop a concept for marine biological valuation which is widely applicable and scientifically acceptable; (2) to develop a protocol around this concept which defines the different steps that need to be taken to develop marine biological valuation maps; (3) to apply the protocol to different case study areas to see how it performs under different circumstances; (4) to review the possibilities of using the protocol for the implementation of several European Directives, which relate to nature conservation in the marine environment, and as part of decision support systems for marine management in general, and spatial planning in particular; and (5) to evaluate the indicator “marine biological value” on its conceptual relevance, feasibility of implementation, response variability and utility for environmental decision-making.