The in situ diet of the pearl oyster Pinctada margarifera was determined in the lagoon of Takapoto Atoll by comparing the phytoplankton composition of water and bivalve gut contents using 2 different methods, optical microscopy and HPLC pigment analysis. In order to evaluate the available food resources for pearl oysters in the water column, a new method for estimating the pigment/chlorophyll a (chl a) ratio (based on an inverse analysis) was developed which allowed us to determine the contribution of the main phytoplanktonic groups in terms of chi a. In the water, picocyanobacteria and nanoflagellates predominated, the latter being mainly chlorophytes and prymnesiophytes. Comparisons between the results obtained by the 2 methods of investigation indicated that most of the dinoflagellates are unpigmented and, therefore, heterotrophic. An examination of the gut contents showed that picocyanobacteria were only weakly ingested by the oyster and, thus, nanoflagellates constituted the main food resource. Cryptophytes, although poorly represented in the water, were preferentially ingested. Chlorophytes were inefficiently digested since they were found alive and motile in the faeces of the oyster. The ecological implications of this feeding behaviour are discussed.