Pearl oysters are farmed in oligotrophic tropical atoll lagoons where planktonic communities are dominated by production from cyanobacteria smaller than 2 μm. Paradoxically, the pearl oyster Pinctada margaritifera only retains particles larger than 2 μm. In this study, we assess the relative contribution of hetero/mixotrophic microbiota to the available planktonic resource. In Takapoto Atoll, picocyanobacteria are the dominant biomass (20 μg C l–1). The carbon biomass of ciliates and dinoflagellates ranges from 1 to 24 and 0.5 to 5 μg C l–1 respectively, with a mean of 6 μg C l–1 for ciliates and 2 μg C l–1 for dinoflagellates. The possible retention by P. margaritifera on a natural protist suspension was investigated. Due to its high clearance rates (ca 20 l h–1 g–1) the pearl oyster retained 85 μg C h–1 g–1 from ciliates and 65 μg C h–1 g–1 from dinoflagellates. Conversely, cyanobacteria were not efficiently retained by the bivalve and did not efficiently contribute to its diet. From our experiments, we concluded that hetero/mixotrophic protists rapidly and efficiently process the picoplanktonic resource towards filter-feeders, particularly pearl oysters.