The gene Pitx2 is thought to be a critical transcriptional factor that mediates left-right asymmetry of internal organs in vertebrates. To demonstrate whether the metamorphic L/R asymmetry is regulated by the left-specific activity of Pitx2, cDNA of Pitx2 gene was amplified from the total RNA of head tissue of metamorphosing Japanese flounder, by reverse transcription polymerase chain reaction (RT-PCR), and different expression of Pitx2 was examined in developing flounder larvae by using relative quantitative RT-PCR, which used 18s rRNA as internal standard. Results from cloning and sequencing show that Pitx2 expression also exists in metamorphosis of Japanese flounder. Results from relative quantification show that a role of Pitx2 as a left determinant is probably played in early stage of metamorphosis. However, it remains to be clarified whether the right eye migration is determined by the left-specific activity of Pitx2 and whether the visceral and the metamorphic L/R asymmetries possess the common molecular mechanisms.