Coastal marine areas are characterized by the highest values of ecosystem services and by multiple uses that are often in conflict with each other. Natural capital analysis is claimed to be a valid tool to support space planning. In the context of the Marine Strategy Framework Directive (MSFD) of the European Union (EU), the EU Joint Research Centre (JRC) Scientific and Policy Report 2014 defines the monitoring of specific descriptors and their possible use, based on an ecosystem-services approach. Mediterranean marine ecosystems are characterized by high biodiversity and the presence of relevant benthic biocenosis that can be used as a tool to support coastal planning, conservation, and monitoring programs. In this study, we considered the Mediterranean benthic biocenosis, as classified by Pérès and Picard, as a working tool and propose a basic spatial unit for the assessment of marine ecosystem services. Focusing on a high-resolution local-scale analysis, this work presents an accurate identification of the different biocenoses for the coastal area of Civitavecchia in the Northern Tyrrhenian Sea, Italy, and ecosystem services, as well as a benefits assessment, of the Posidonia oceanica meadows.