In conclusion, this study allowed us to (1) Obtain over 14538 unigenes from L. vannamei, (2) Compare the transcriptomes between WSSV-infected and uninfected shrimp, and (3) Identify potential pathways and candidate genes involved in L. vannamei response to WSSV infection. Further studies on the functionality of these genes will provide valuable information on the antiviral mechanism in shrimp.