Italian Marine Protected Areas (MPAs) are multiple objective, aiming to ensure environmental conservation and the sustainable use of marine and coastal resources. Italy has established 22 national MPAs and 28 more are foreseen by law. This national MPA system requires a standardised design approach. Zoning is the first tool applied to regulate human activities, focusing on conservation and the separation of usage conflicts. A multiple-use zoning should provide high protection to noteworthy natural areas and identify suitable zones for environmentally sustainable activities. ICRAM has conceived a specific GIS-Decision Support Tool (GIS-DST) as support to the Italian Ministry of Environment in the zoning of MPAs. This tool provides a comprehensible, reasonable and repeatable analysis process which clearly displays the final results. The GIS-DST integrates the following guidelines: the zoning plan must be of straightforward application; fragmentation among the zones must be minimal; boundaries must be based on easily identifiable land based points of reference; levels of protection must decrease progressively from maximum protection to unrestricted zones. The GIS-DST is conceived to assist decision makers in identifying priorities and facilitating the relations with the stakeholders. This tool delineates a comprehensive picture of all the environmental and socio-economic values and of their relative importance and helps the exchange of views with the stakeholders by clearly visualising the priorities and values.