High-throughput sequencing was performed on adductor muscle (Ad for short), gill (Gi for short), mantle (Ma for short) and gonad (Go for short) tissues of 1-year and 3-year Pinctada fucata by Illumina HiSeq 4000 platform. PIWI genes, which contribute to piRNA biogenesis in P. fucata, were assembled based on the annotated results. The relative expression of PIWI genes were calculated according to transcripts per kilobase million mapped reads (TPM) method at different development stage and sexual.