Baculovirus associated with white spot syndrome (WSBV) is the causative agent of a disease with high mortalities and causes severe damage to shrimp cultures. In this study, we analyzed a recombinant clone (E3) obtained from a viral genomic library to characterize the causative agent in diseased shrimp Penaeus chinensis with white spot syndrome. According to the analysis of nucleotide sequence of E3, this clone did not showed considerable sequence homology with those of other known viruses, including baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV), indicating that WSBV is a novel virus causing a serious disease in P. chinensis. Based on the sequence of E3 clone, a pair of PCR primers was designed. After 30 cycles of amplification, a specific product of the expected size was detected only if the total nucleic acids extracted from the diseased shrimp was used as a template DNA, suggesting that this method can be used to diagnose the virus infection in diseased shrimp.