Molecular techniques are now essential for discovering new functional genes for the improvement of cultured marine organisms. Such techniques can be used to obtain expressed sequence tags (EST) and, through the use of microarrays, the entire transcriptome. For example, microarrays can be used to reveal biomarkers of health conditions, nutrient changes and immune response in fish and shellfish. EST-based microarray chips were constructed for cultured fish and shellfish species including Japanese flounder (Paralichthys olivaceus). Using the flounder microarray chip, the efficacy of two DNA vaccines derived from pathogenic viruses [hirame rhabdovirus (HRV) and viral hemorrhagic septicemia virus (VHSV)] was evaluated through gene expression profiles. The results suggest that both DNA vaccines were effective in protecting the flounder from HIRRV and VHSV. The flounder microarray was also used to compare gene expression patterns in fish that are susceptible and resistant to Edwardsiella tarda. At 3days post infection, the gene expression patterns between the two groups were dramatically changed. Thus, microarray analysis is a very powerful tool to understand gene expression profiles in fish.