The Mediterranean basin is recognized as one of the most diverse regions on the planet, but is being threatened by overexploitation and habitat loss. Furthermore, the Strait of Gibraltar and adjacent Alboran Sea have been identified as representing an important habitat for many threatened or endangered species. In this context, one vehicle for marine conservation is the creation of marine protected sites, although Mediterranean Marine Protected Areas (MPAs) are neither large nor representative enough to form an effective network of protection. An inventory of the benthic communities and habitats of conservation interest has been carried out in Cap des Trois Fourches, an ecological and biogeographical site of interest. Univariate and multivariate analyses showed differences for marine communities among habitats and localities, indicating a great diversity in marine assemblages but an absence of a spatial gradient in marine α-diversity. The Trois Fourches area showed a high environmental quality and hosted several endangered species. Habitats of conservation concern, such as marine caves, seagrass meadows and coralligenous assemblages, were detected and studied. The scientific data recorded provide sound support for the establishment of a new MPA in Trois Fourches, taking into account that the findings match the scientific criteria required for declaration as a protected area. The benefits for connectivity at the Mediterranean scale and the local economy are discussed.