In many cases, government institutions insufficiently consider the traditional land use of community areas in spatial planning policy. Although numerous investigations into the participatory mapping of community lands have occurred, their results have not been adequately incorporated into the policy realm. In Indonesia, Spatial Planning Regulation (SPR), or locally known as Rencana Tata Ruang Wilayah (RTRW) is an instrument to guide land use practices in the categories of development and protected areas. Using a case study for the Merauke district in Papua province in Indonesia, we demonstrate how participatory mapping results of important community areas were integrated into district-level spatial planning through Participatory GIS (PGIS). There are three phases to the process of integrating PGIS into Spatial Planning Regulation. The first phase is to develop a shared vision between the customary communities and the district government and gain a commitment from both parties to use the results in further planning processes. The second phase is to facilitate the PGIS process, which is conducted by the community and a facilitator -in this case a team of WWF Indonesia Sahul Papua Region Office -, and the final phase is to integrate the PGIS results of the important community areas into spatial planning regulation. The results of our case study showed that of the total area adopted by the RTRW, about 69% were important community areas designated as cultural preservation areas. The remaining important community areas were allocated to two other land use categories: protected areas (22%) and development areas (9%). In this case, 91% of the community areas (647,850 hectares) were secured from other land use purposes such as large-scale agriculture, mining, forestry, and infrastructure. The PGIS approach can be applied to districts across Indonesia for mapping community land use practices and integrating them into Spatial Planning Regulation.