The pearl oyster, Pinctada fucata, is an important economic shellfish, and its larva is an ideal model in which to study the molecular mechanisms of larval development in invertebrates. The development of larva would directly affect the yield and quality of pearl oyster. Increasing evidence suggests that microRNA(miRNA)s play an important role in development. However, the knowledge of the effects of miRNA expression on the early development of P. fucata is still limited. In this study, we analyzed the mRNA and miRNA transcriptomics in seven different developmental stages of P. fucata using Illumina RNA sequencing.