Flatfish such as the Atlantic halibut (Hippoglossus hippoglossus) undergo a dramatic metamorphosis that transforms the pelagic, symmetric larva into a benthic, cranially asymmetric juvenile. In common with amphibian metamorphosis, flatfish metamorphosis is under endocrine control with thyroid hormones being particularly important. In this report we confirm that tri-iodothyronine (T(3)) levels peak at metamorphic climax during halibut metamorphosis. Moreover, we have isolated cDNA clones of TRalpha and TRbeta genes and confirmed the presence in halibut of two TRalpha isoforms (representing the products of distinct genes) and two TRbeta isoforms (generated from a single gene by alternative splicing). Real-time PCR was used to assess expression of these genes during metamorphosis. TRbeta shows the most dramatic expression profile, with a peak occurring during metamorphic climax.