Coralligenous habitats are part of the most important Mediterranean marine ecosystems in terms of complexity and biodiversity. They provide protection, feeding and reproduction areas for more than 1600 species. This biodiversity is essential for economic activities such as fishing and scuba diving. The European program CIGESMED (ERA-NET funding), involving France, Greece and Turkey, investigates the “Good Environmental Status” of these habitats in the framework of the MFSD (Marine Strategy Framework Directive). One major objective of CIGESMED is to propose an operational, long-term, large-scale protocol to monitor coralligenous habitats in the Mediterranean Sea. This protocol is currently tested in French sites: the effects of (sampling) methods, materials and operators are studied in order to evaluate the influence of protocol implementation, and to find the easiest and most reliable procedure that could be implemented by and for a large public, also consisting of non-scientists, and would provide workable data for longterm monitoring. This protocol is based on photo-quadrats observations. The analyses are done on occurrences, relative abundances, species associations and species’ favourite environmental profile. In parallel, complementary protocols are implemented: one concerns the cartography of coralligenous habitats, and two are about population genetics of significant habitat-forming species Myriapora truncata (Pallas, 1766) and Lithophyllum cabiochiae ((Areschoug) Hauck, 1877)). All the data and results are organized as a non-centralized information system, with configurable plugins that can be installed free by all new partners