Two distinct TR alpha cDNA clones (TR alpha A and TR alpha B) were isolated from conger eel (Conger myriaster). The deduced amino acid sequences of the conger eel TR alphas showed higher homologies to the TR alphas of other vertebrates than to TR betas. Determination of TR mRNA in metamorphosing eels was performed using competitive RT-PCR. Of the two TR alpha mRNAs identified, TR alpha A mRNA expression was shown to be relatively higher than that of TR alpha B, and there was a peak in the expression of each during metamorphic climax. We hypothesize that both TR alphas play important roles in morphological differentiation during metamorphosis. The expression pattern of TR beta 1 mRNA was also higher during metamorphic climax and high levels of expression continued after metamorphosis. This suggests that TR beta 1 is the adult fish form which appears at high frequency after metamorphosis. It was also shown that TR beta 2 is highly expressed specifically in the brain and pituitary gland in larvae and juvenile forms including during metamorphosis and there was a peak in TR beta 2 mRNA in the elver after metamorphosis. Thus, we propose that TR beta 2 plays an important role in the regulation of the hypothalamic-pituitary-thyroid axis.