In a human-altered marine environment, fragmented and subjected to unprecedented climate change, planning sustainable strategies for development requires to understand the distribution of marine biodiversity and how its variations impact ecosystem functioning and the evolution of species. Functional Connectivity characterizes the migratory flows of organisms in the landscape. As such, it determines the ecological and evolutionary interdependency of populations, and ultimately the fate of species and ecosystems. Gathering effective knowledge on Marine Functional Connectivity (MFC) can therefore improve predictions of environmental change impacts and help refine management and conservation strategies for the Seas. This is challenging though, because marine ecosystems are particularly difficult to access and survey. Currently, >50 institutions investigate MFC in Europe, by using complementary methods from multiple research fields to describe the ecology and genetics of marine species. SEA-UNICORN aims at coordinating their research to unify the varied approaches to MFC and integrate them under a common conceptual and analytical framework for improved management of marine resources and ecosystems. For this, it will bring together a diverse group of scientists in order to collate existing MFC data, identify knowledge gaps, reduce overlap among disciplines, and devise common approaches to MFC. It will promote their interaction with connectivity theoreticians and ecosystem modelers, to facilitate the incorporation of MFC data into the projection models used to identify priorities for marine conservation. Lastly, it will forge strong working links between scientists, policy-makers and stakeholders to promote the integration of MFC knowledge into decision support tools for marine management and environmental policies.