As with most cultivated bivalves, culture of the Tahitian pearl oyster Pinctada margaritifera is particularly dependent on the natural environment, especially for spat supply. The ability to track in real time the abundance and the development of pearl oyster larvae in the plankton would help optimize spat collection in atolls of French Polynesia. However no identification criteria are available for the larvae of several bivalves species present in the lagoons and it is not yet possible to specifically monitor pearl oyster larvae. The aim of this study is to determine the most pertinent morphological identification criteria, to specifically identify the larvae of P. margaritifera and differentiate them from those of three other abundant species: Pinctada maculata, Crassostrea cuculata and Chama sp. The method of image analysis after photon microscopy was assessed. It allowed automatic measurement of numerous morphometric features that were tested alone or in combination and identification threshold for P. margaritifera larvae were determined by statistical analyses. These results led to a key that allowed correct identification for 77% of P. margaritifera larvae. The hinge diagnosis method under scanning electron microscopy, a prime method for the identification of specific criteria oil bivalve larva shells, was also used on larvae of both Pinctada species. The two species could be differentiated precisely because of specific differences in the thickness of their hinge provinculum and the number of denticles it bears. However this approach is too time-consuming and technically demanding to use in real time field studies. This study showed the limitations of image analysis as an identification tool of the P. margaritifera larvae, but proper statistical analyses and especially the decision tree approach could be used to evaluate and efficiently prioritize the choice of the species identification criteria.