Apoptosis is a normal process for regulating cellular death of many organisms. Here, we molecularly characterized an inhibitor of apoptosis from Schistosoma japonicum (SjIAP). The transcription of the SjIAP predominantly occurred at the developmental stages in a final host. Functional assay indicated that the SjIAP could inhibit caspase activity either in 293T cell or in schistosome lysates. Additionally, there were differently expressed profiles of the SjIAP in S. japonicum living in different hosts. Our preliminary results suggest that the SjIAP may play important roles in parasitic living and development as well as in the host-parasite interactions, and drug target of SjIAP might be a potential for controlling schistosomiasis.