The knowledge of small-scale fisheries (SSFs) is important to develop management policies and mitigate the competition for marine resources. However, spatially explicit information is often unavailable at the regional and subregional scale. We designed and tested a novel participatory approach to map the SSF fishing effort using the Mediterranean sea as a case study. We applied the approach in eight countries (Albania, Croatia, Italy, Libya, Malta, Montenegro, Slovenia and Tunisia) characterized by different cultural, social, political and ecological features. The results provided quantitative and spatially explicit information on fishing operations on a fine-scale resolution, contributing to overcome the pragmatic and budgetary constraints that to date have prevented an accurate assessment of SSFs worldwide. This novel participatory approach is inspired by the principles of governance, adaptive management, cross-national cooperation and spatial planning, thus supporting the ecosystem approach to fisheries and has the potential to provide a useful complement to traditional assessments.