The southern coastal zone of the Atacama Desert, mainly in the Caldera and Copiapó area, is known for its geomorphological and paleontological features that are recognized nationally and internationally by their geoheritage significance. In this context, a zoning of the territory was carried on, which main objective was to generate a scientific base that takes into account the intrinsic value of these natural elements and that will allow an integrated land use management of this zone. The coastal area is characterized by fossiliferous marine terraces, coastal dunes and particularly by the great Dune Sea located in the coastal range of Copiapó, in addition to protected marine and coastal areas, as Isla Grande de Atacama. In this way, territorial units ranked by its geoheritage value, were determined using a multicriteria analysis methodology, that integrates different spatial variables as geomorphology, location of geosites, coastal vegetation and existing protected areas. Higher valued territorial units resulted to be the dune sea, paleontological sites, fossiliferous cliffs and the wetland of the estuary of the Copiapó river. In particular, the dune sea, forms a remarkable scenic landscape of regional and national importance and this geoheritage component of the coastal desert of northern Chile, jointly with the other highly valorized features, should be considered in the proposals for integrated management of the coastal zone.