Yellowtail is widely distributed in the northwest Pacific Ocean, from Japan to Hawaii and important aquaculture fish in Japan. For functional gene identification for biological traits and breeding yellowtail by marker-assisted selection (MAS) or gene-assisted selection (GAS), we carried out tanscriptome analysis of one female yellowtail using Roche/454 GS FLX Titanium platform to construct reference sequence of expression genes. Already, we reported fine radiation hybrid (RH) physical map with 1,531 markers. If we will map many EST sequence on the RH physical map newly and construct high-density physical map, we will be able to compare chromosome structure and synteny with model fish and another fish species correctly.