Individual habitat maps from surveys provided by EMODNet Seabed Habitats with the distribution of the bioconstruction along the Apulian coasts are not well known and, in some areas, totally unknown. This is particularly evident for the Coralligenous assemblages. Furthermore, a regional scale georeferenced cartography is not yet available and the knowledge of the cliffs is really poor. The aim of the Biomap project, started in 2013, is to fill this gap by providing an effective cartography tool for the evaluation of the already instituted Sites of Conservation Interest (SCIs). High resolution acoustic data (MBES multibeam echosounder), seismic profiles (Chirp sonar and sub-bottom profiler) and ROV images were acquired for the habitat mapping within 3 MPAs and 21 SCIs up to 100m depth. Furthermore, data acquired outside the above mentioned protected areas were used in specific deeper zones (up to 700m depth).