The veined rapa whelk (Rapana venosa) is widely consumed in China but is also a predator that is reducing bivalves resources in oceans worldwide. Larval metamorphosis of this species, a pelagic to benthic transition that involves considerable structural and physiological changes, plays a pivotal role in its commercial breeding and natural populations. Thus, the endogenous microRNA that drive this transition attract considerable interest. This study is the first to investigate alterations of miRNA expression during metamorphosis in a marine gastropod by using high-throughput sequencing. A total of 195 differentially expressed miRNAs were obtained, including 65 miRNAs differentially expressed during the transition from pre-competent larva to competent larva (33 up-regulated and 32 down regulated) and 123 miRNAs differentially expressed during competent to post larva transition (96 up-regulated and 27 down regulated). Our data improve understanding of the microRNA function into R. venosa metamorphosis and provide a solid basis for further study. Overall design: Larval samples from pre-competent larval stage (the three spiral whorls stage), competent larval stage (the four spiral whorls stage) and the post larval stage (juveniles) were collected with three biological replicates (each replicate contains 40~100 individuals).Total RNA was extracted from an individual intestine using the RNeasyMini Kit (Qiagen, USA) according to the manufacturer's instructions. The quality and concentration of RNA were measured using a NanoDrop 1000 spectrophotometer (Thermo). After total RNA extraction, the RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gel electrophoresis (PAGE). Then the 3’adapters were added and the 36-44nt RNAs were enriched. The 5’adapters were then ligated to the RNAs as well. The ligation products were reverse transcripted by PCR amplification and the 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. Limited (Guangzhou, China).