Identifying vulnerable habitats is necessary to designing and prioritizing efficient marine protected areas (MPAs) to sustain the renewal of living marine resources. However, vulnerable habitats rarely become MPAs due to conflicting interests such as fishing. We propose a spatial framework to help researchers and managers determine optimal conservation areas in a multi-species fishery, while also considering the economic relevance these species may have in a given society, even in data poor situations. We first set different ecological criteria (i.e. species resilience, vulnerability and trophic level) to identify optimal areas for conservation and restoration efforts, which was based on a traditional conservationist approach. We then identified the most economically relevant sites, where the bulk of fishery profits come from. We overlapped the ecologically and economically relevant areas using different thresholds. By ranking the level of overlap between the sites, representing different levels of conflicts between traditional conservation and fishing interests, we suggest alternatives that could increase fishers' acceptance of protected areas. The introduction of some flexibility in the way conservation targets are established could contribute to reaching a middle ground where biological concerns are integrated with economic demands from the fishing sector.