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The Centre is scientifically organized in three Research Lines (Global Changes and Ecosystems Services, Marine Biotechnology and Biology, Aquaculture and Seafood Quality), which are subdivided in 10 Research Groups and 28 Research Teams. Each Research Group contributes with actions and scientific output that may fit into one or more Research Lines.

CIIMAR implements various Transversal Programmes to strengthen the interdisciplinary collaboration between the various teams.