Caspases are central effectors in apoptosis. In this investigation, a novel caspase gene (designated as PjCaspase) obtained from the marine shrimp Marsupenaeus japonicus was found to be significantly upregulated in survivors of WSSV-challenged shrimp, suggesting that it might be involved in shrimp antiviral immunity. As revealed by RNAi assays, when the PjCaspase gene was silenced by gene-specific siRNA, the WSSV-induced apoptosis was significantly inhibited. The results showed that the PjCaspase gene was essential in the virus-induced apoptosis of shrimp. Based on the quantitative PCR detection, it was shown that the PjCaspase gene silencing resulted in the increase of virus copies, indicating that apoptosis played a key role in antiviral process of shrimp. As well known, caspase-3 and -8 are crucial caspases in apoptosis. The discovery of PjCaspase in this study would contribute another essential caspase involved in apoptosis against virus infection, which might reveal an ancient mechanism of caspase activation in invertebrate immunity against viruses.