A decision support tool was used to determine priority sites for marine conservation within the Isla Grande de Atacama multiple uses marine protected area (MUMPA) in northern Chile, based on both biological and social information. Scuba diving, and an unweighted paired-group method using arithmetic average (UPGMA) analyses were used to determine the main benthic communities found in the shallow rocky and soft-sediment subtidal. To establish the costs of conservation, a social survey was undertaken to identify major users, uses and localities within the MUMPA. A multi-layer database with biological, physical, and social information was generated and further defined 28 approximately 70ha analysis units. Explicit conservation criteria were then determined and four conservation goals defined (protection of 10, 20, 50, and 70% of each of the communities). Seven rocky reef and three soft-sediment communities were identified in the shallow subtidal. Four of the 28 units had high costs of conservation owing to high frequency of use by fishermen, divers, and algae harvesters (main users). These areas represented the highest risks for potential conflicts with the main users. Under the conservation goals of 10% and 20%, 36.8 and 44.4% of the whole marine area were selected as priority areas for protection respectively. The units selected presented low and medium costs of conservation, thus they had low risks of potential conflicts with users. This is the first study that uses a decision support tool to identify priority sites (i.e. units) in the shallow subtidal based on benthic communities and also incorporates social aspects to assess conservation costs. The use of social aspects enables the establishment of management strategies that agree both with biodiversity conservation and socio-economic development of fishing communities. This approach can be replicated for the planning of other coastal MPAs where artisanal fisheries and tourist activities co-occur and interact with conservation efforts. Copyright (C) 2011 John Wiley & Sons, Ltd.