Coralligenous habitats are bioconstructed, emblematic habitats of the Mediterranean Sea, which display a remarkably complex tridimensional structure and are considered as one of the most important biodiversity hotspots of the Mediterranean Sea. In order to assess the specific diversity of these habitats we sampled small surfaces (10 cm 2) of these habitats using a suction sampler in different environmental conditions on 19 sites in the Marseilles area (France). These samples were crushed and total DNA was extracted. A small portion of the COI gene was amplified using universal primers targeting metazoans. A total of 3029 Molecular Operationnal Taxonomic Units (mOTUs) were found among all samples. Most of the mOTUs belong to three taxonomic groups: Rhodophyta, Arthropoda and Annelida but many other phyla were detected. Environmental factors such as depth, slope and locality influence the community composition of coralligenous habitats. This first assessment of the specific diversity of these habitats using a metabarcoding approach confirms the status of biodiversity hotspot of these habitats and underlines the importance of abiotic variables to structure the community. Methodological developments can be used to design new monitoring protocols of these habitats.