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 TRα and TRβ genes and confirmed the presence in halibut of two TRα isoforms (representing the products of distinct genes) and two TRβ isoforms (generated from a single gene by alternative splicing). Real-time PCR was used to assess expression of these genes during metamorphosis. TRβ shows the most dramatic expression profile, with a peak occurring during metamorphic climax.