An original data set of 556 benthic mollusc taxa, as a first account of Cape Milazzo local biodiversity, is provided. Qualitative differences between more or less anthropized areas have been put in evidence, and species distribution according to the main habitat typologies has been detailed. The highest biodiversity was found in the northern sites, corresponding to the Zone A of the established marine protected area. Most mollusc species under the European Economic Community (EEC) and National protection, and other ones listed as threatened, have been recorded, and are mainly associated to priority habitats as phanerogams meadows and vermitid reefs. In the meantime, the settlement of not indigenous species, mainly of tropical origin, and disease affecting threatened organisms under EEC protection, testified the vulnerability of the local ecosystem under the global change threat.