Pearl farming, the second principal economic resource for French Polynesia, is based on the exploitation of the blacklip pearl oyster Pinctada margaritifera (Mollusca, lophotrochozoa) which is a protandrous hermaphrodite species: at the first maturation all oysters are males and the female sex appears progressively from around two years old to eventually reach a 1:1 sex-ratio. Today, genetic bases of sexual determinism and sexual differentiation including their molecular pathways in pearl oyster are still unknown. To better understand these molecular mechanisms whereby gene expression may act in sexual dimorphism and to develop a database for future reproduction studies, we performed a gonad transcriptomic analysis of this commercially important species.