Retinoic acid (RA) regulates expression of various genes critical for vertebrate development. In flounder, RA exposure of metamorphosing larvae causes fusion of centra and ectopic pigmentation of blind-side, presumably by disturbing expression of RA-target genes. To approach the molecular mechanism underlying the malformation induced by RA, we intended to identify up- and down-regulated genes by RA using RNA-seq transcriptome analysis. Comparison of expression profile between RA-treated and control revealed up-regulated and down-regulated genes. Our RNA-seq data would help understanding the molecular basis of the RA-induced abnormalities and the functions of endogenous RA in the flounder metamorphosis.