In order to unravel the miRNAs and piRNAs expression patterns in molluscs, we generated a comprehensive small RNA dataset by small RNA sequencing (sRNA-seq) of numerous molluscs to discovered the small RNAs both of miRNAs and piRNAs in the somatic and gonadal tissues of molluscs, which would serve as an important reference data for genomic and genetic studies of small RNAs in molluscs.