Given the frequent socioeconomic, political and concomitant ecological failures of science-driven marine protected area (MPA) programmes, it is now important to design MPAs by integrating natural and social science research more comprehensively. This study shows how indigenous peoples assisted in the design of MPAs by identifying marine substrates and related resident taxa on aerial photos, information which was then incorporated into a geographical information system (GIS) database, along with dive survey data. Two questions were asked: (1) Is indigenous ecological knowledge accurate enough for mapping the benthos and associated taxa? (2) Is such an approach an appropriate way for assisting in the biological and social design of MPAs in Oceania? Conventional quadrat field dive surveys were used to measure the accuracy of substrate identification by local informants and a visual survey was used to test hypotheses formulated from local knowledge regarding the spatial distribution and relative abundance of non-cryptic species within certain benthic habitats. Equivalence rates between indigenous aerial photo interpretations of dominant benthic substrates and in situ dive surveys were 75–85% for a moderately detailed classification scheme of the benthos, which included nine locally-defined abiotic and biotic benthic classes for the MPA seabed. Similarly, the taxa inventory showed a strong correspondence between the qualitative predictions of local fisherfolk and the quantitative analysis of non-cryptic species distribution, including their relative abundance and geophysical locations. Indigenous people's predictions about the presence or absence of fish in different benthic habitats corresponded 77% and 92% of the time (depending on scoring schema) with in situ visual measurements. These results demonstrate how incorporating local knowledge of benthic heterogeneity, existing biological communities, and particular spatio-temporal events of biological significance into a GIS database can corroborate the production of scientifically reliable base resource maps for designing MPAs in an environmentally and culturally sound fashion. This participatory approach was used to design and then establish MPAs in the Roviana and Vonavona region of the Western Solomon Islands. Under appropriate conditions, interdisciplinary work can complement the design of scientific fishery management and biodiversity conservation prescriptions for coastal Oceania.