In 2015, the Strait of Sicily, which includes several banks, was candidate as a future Specially Protected Area of Mediterranean Importance (SPAMI) by the Contracting Parties of the Barcelona Convention. In this context, the present study aims to provide the first biological and ecological characterisation of this poorly known area, focusing on habitats and species of conservation concern. Surveys were carried through a remotely operated vehicle (ROV) and allowed the identification of 19 habitat types, mostly considered of priority interest by the SPA/BD Protocol of the Barcelona Convention. A total of 269 taxa were also identified, mostly Porifera, Cnidaria and Pisces, among which 115 species are of conservation concern according to the International Union for Conservation of Nature (IUCN) Red Lists, the Habitats Directive, the Bern Convention, the SPA/BD Protocol and CITES. ROV surveys allowed some interesting observations on poorly known species and habitats. Results underlined that remarkable discrepancies in species conservation status assessment that exist between the several lists of protected species considered. The IUCN Red Lists, although not legally binding for European States, are the most complete, but, in spite of this, the conservation policies in the EU are largely focused on the Habitats Directive, which is really not exhaustive. An exhaustive and legally binding instrument to protect species of conservation concern at European scale is highly recommended. Acquired results could be useful for the delimitation of a future SPAMI or a network of Marine Protected Areas (including the investigated banks) and the identification of zones within them suitable for different area-based management measures.