High human reliance on marine resources in developing countries is a challenge for implementing marine protected areas, which usually seek to limit or restrict fishing in selected areas. Fishers’ spatial preferences should be considered during the site selection process, but biodiversity considerations are generally the primary focus. The Protected Area Suitability Index (PASI) is a fuzzy logic spatial planning tool that combines human preferences and conservation criteria to assess the suitability of marine sites for being protected from fishing and other extractive use. We apply the PASI in zoning a marine sanctuary in Sabah, Malaysia, with the objectives of i) assessing the PASI’s ability to capture fishers’ spatial preferences; and ii) comparing the nuances of community based and fuzzy logic approaches in spatial planning. There was overlap in sites chosen for protection by both approaches, and multi-dimensional scaling results suggest that the PASI captures fishers’ preferences. Community consultations enable direct integration of local knowledge to fill gaps in scientific knowledge, but can be time consuming and expensive. The PASI is an alternative to data and labour intensive conservation planning tools that are currently available, and can be particularly useful for zoning marine protected areas in data poor developing countries where conservation requires quick action.