Two distinct cDNAs encoding thyroid hormone receptors (THRs) were cloned from a lambda gt10 library prepared from the whole bodies of metamorphosing flounder larvae (Paralichthys olivaceus). Deduced amino acid sequences of the two isolated cDNAs shared 96% and 92% homologies in their DNA- and hormone-binding domains, respectively. These were highly conserved when compared to THRs for other vertebrates: 88-96% in the DNA-binding domain and 84-94% in the hormone-binding domain. Other receptors in the nuclear receptor family showed lower homologies than those of THRs. Both THRs for the flounder had higher homologies with the alpha-type THRs of other vertebrates than with the beta-type. Thus, the two THRs for flounder were designated as fTHR alpha A and fTHR alpha B.