Greater amberjack (Seriola dumerili) is widely distributed in tropical and temperate waters of whole world and important aquaculture fish. For functional gene identification for biological traits and breeding amberjack by marker-assisted selection (MAS) or gene-assisted selection (GAS), we carried out comprehensive transcriptome analysis of greater amberjack using next-sequencing technology to detect SNPs in expression sequences. We mixed twelve tissues (muscle, brain, eye, heart, liver, intestine, kidney, spleen, gonad, gill, fin and bladder) extracted total RNA from these tissues, synthesized cDNA from total RNA by N6 randomized primer. Normalization was carried out by one cycle of denaturation and re-association of the cDNA.