The Marine Strategy Framework Directive (MSFD) defines monitoring goals for coralligenous environments as well as their good environmental status assessment within the Mediterranean by 2016. Developing methods to monitor and evaluate challenging ecosystems at multiple scales is a necessity and advance to achieve these goals. Habitat distribution modelling and remote sensing techniques are important tools for ecosystem based management, conservation planning and impact assessments. Therefore, we aimed to analyse the performance of the Maximum Entropy approach (MaxEnt freeware) for modelling the distribution of coralligenous habitats. We built the habitat suitability models using i) presence data collected in the Portofino Marine Protected Area (Ligurian sea) and, ii) geophysical substrate properties extracted from multibeam sonar measures (depth, slope, aspect, rugosity, and geomorphic zones) to allocate known coralligenous communities in the MPA and to forecast new undescribed areas. We conclude that predictions based on combined model results provide more realistic estimates of the core area suitable for coralligenous environments and should be the modelling approach implemented in conservation planning, monitoring activities and management.