At 6 h post challenge (HPC), a total of 806 clones showed differential expression profile in WSSV-challenged samples but not in Vibrio-challenged samples. The structural proteins (DD9A, cuticle protein AMPIA), phosphopyruvate hydratase, arginine kinase, and hemocyanin were the significantly downregulated elements in the samples of 6 HPC, whereas alpha tubulin was the most significantly upregulated one.