CIESM is served by a number of instances represented in the schematic diagram below:

This is the central decision-making body of the Commission.  Brings together once a year  the National Delegates of 22 Member States. Chaired by the President, H.S.H. Prince Albert II of Monaco, assisted by the Director General.

Advises on the strategic, mainly scientific, orientations of the Commission. Meets once a year. Composed of the President, the Director General, and the National Delegates of eight countries elected by the Board during each Congress: currently Croatia, France, Israel, Italy, Monaco, Spain, Tunisia and Turkey.

Is appointed by the Board to manage the overall work of the Commission. Pays particular attention to the coordination of all scientific issues and to the development of international cooperation. The post is held by Professor Frederic Briand.

There are six scientific committees, comprising Marine Geosciences, Physics and Climate of the Ocean, Marine Biogeochemistry, Marine Microbiology and Biotechnology, Living Resources and Marine Ecosystems, Coastal Systems. Their Presidents are elected for a three-year term at each Congress and rely on the cooperation of over 2000 researchers based in Mediterranean marine institutes as well as northern Europe and oversea.

Seven/eight programs, each headed by a coordinator, monitor the changes or trends in critical parameters across the whole Mediterranean Basin.  They include at the moment Hydrochanges, JellyWatch, Marine Economics, MedGLOSS, Mediterranean Exotic Species, PartnerSHIPS and Tropical Signals.