Cystatins (CSTs) belong to a protein superfamily the members of which reversibly bind cysteine proteases and inhibit their activity. CSTs are divided into three families:family 1 CSTs are single domain cystatins that do not contain disulfide bridges and carbohydrate side chains; family 2 CSTs possess a single cystatin domain, but their structures have at least two intramolecular disulfide bridges; and family 3 CSTs display a higher degree of structural complexity characterized by the occurrence of multiple cystatin-like domains, each with two disulfide bridges at positions homologous to those in family 2 CSTs. CSTs widely occur in various vertebrates such as mammals, birds, and fishes. CSTs have also been identified in some invertebrates. In many cellular defense systems, the CSTs plays a role in preventing the excessive hydrolysis of cellular proteins by cysteine proteases, and regulate many metabolic processes that depend on cysteine proteases. However, the study of the role of CSTs in the gonads of animals has not yet been reported. is a member of the Palaemonidae family of decapod crustaceans and is widely farmed in China because of its flavor and high nutritive and economic values. To breed superior variety of during actual production, it is necessary to study the characteristics and functions of the gonadal development-related genes of this species. The aims of this study were to identify the sequence information and function of CSTs in the ovary of CST (MnCST) cDNA sequence was cloned using the rapid amplification of cDNA ends (RACE) technology; then, real-time quantitative PCR (RT-qPCR) was used to analyze the expression level of in different tissues and different developmental stages of the ovary; and finally, the role of MnCST in the ovary of was analyzed by RNA interference (RNAi) technology. The results showed that the full-length cDNA of was 6199 bp long, including 1183 bp at the 5'-UTR, 2304 bp at the 3'-UTR, and a 2709 bp open reading frame encoding a peptide of 903 amino acids. The putative peptide contained six cystatin-like domains and 42 phosphorylation sites. Multiple sequence comparison of crustacean CST indicated that MnCST has the highest similarity with the corresponding protein in , while it has the lowest similarity with the corresponding protein in mRNA in nine different tissues of , and the maximum level was detected in the intestine. Moreover, M. nipponense ovary; the maximum level was detected in the stage IV ovary, while the minimum level was detected in the stage Ⅱ ovary. The results of RNAi showed that the expression change of the gene was basically consistent with the expression changes of cathepsin B (M. nipponense, while there was no effect on the expression of vitellogenin ( is likely to inhibit the activities of cathepsins and indirectly regulate the hydrolysis of Vg during ovarian development. This study provides new insights into the role of CSTs in the gonads of crustaceans.