Spatial conservation prioritization is used worldwide for designing marine protected areas (MPA) that achieve set conservation objectives with minimal impacts to marine users. People involved in small-scale fisheries (SSF) may incur negative and disproportionate impacts from implementing MPAs, yet limited available data often restricts their representation in MPA planning. Using a Philippines case study, we focus here on the systematic design of a MPA network that aims to minimize and distribute costs equitably for SSF whilst achieving representation targets for biodiversity conservation. The objectives of the study are to: (1) document a participatory mapping approach for collecting SSF data for prioritization using the local knowledge of fishers; and (2) examine how the completeness and resolution of SSF data may affect prioritization outputs in terms of biodiversity representation, spatial efficiency, and distribution equity. In the data-poor region, we conducted participatory mapping workshops with fishers in 79 communities to collect data on the spatial distribution patterns of different SSF fisheries and communities, and employed remote sensing techniques to define coastal habitats, which were targeted for inclusion in MPAs. The datasets were integrated within the decision-support tool Marxan with Zones to develop three scenarios. The SSF data incorporated in each scenario varied based on their completeness (considered all fishing methods or only dominant methods) and resolution (fishing methods itemized by community or municipality). All scenarios derived MPA plans that met representation targets with similar area coverage. The outputs, however, varied in terms of distribution equity, measured by the distribution of opportunity costs (loss of fishing grounds) across different fisheries and communities. Scenarios that did not include minority fisheries or variations between communities, led to inequitable costs. These results highlight the need to incorporate detailed data on SSF at appropriate resolutions, and how this can be achieved through participatory approaches.