Assessment of mangrove ecosystem services (ES) is essential to understand and manage the contribution of these ecosystems to the well-being of local communities. They are the primary beneficiaries but their experience, knowledge, and information are frequently ignored in ES assessment and mapping. In this study, a participatory resource mapping (PRM) approach was applied using local knowledge and experience to analyze geo-referenced information on mangrove ecosystem services. Local communities were involved from the beginning in method selection, application, evaluation, and verification. This “inclusive participatory ES mapping” was conducted in two villages (Bedono and Timbulsloko, Central Java, Indonesia) from 2014 to 2015. Participants representing different community elements were involved in the mapping process. They first created a historical map of the situation in their villages roughly between 1980 and 1999 (before rehabilitation) and then described the subsequent environmental changes. The mapping exercise also documented different mangrove resources that are utilized by communities and identified key areas, such as harvesting zones, biodiversity hotspots, erosion zones, different fishing grounds, and newly rehabilitated areas. The maps reveal that integrating PRM and indigenous geo-referenced information can elicit past and contemporary information on (changes in) ecosystem service availability and use. The results show that by involving local communities from the beginning, the participatory ES mapping can facilitate social learning, provide the foundation for the creation of social capital, and equip the community with sufficient spatial information to improve local mangrove management. The participatory ES mapping approach presented in this paper can be used as a model to support local and regional decision-making processes and to enhance community-based mangrove management in other coastal regions in Indonesia and beyond.