The circadian-expressed luciferin-binding protein from the dinoflagellate Gonyaulax polyedra is regulated at the translational level. We detected a protein, apparently a dimer, that binds specifically to the 3' untranslated region of its mRNA. Its binding site was localized within a 22-nt region in the 3' untranslated region containing seven UG repeats. The binding activity of this protein cycles on a daily basis, decreasing at the beginning of the night when synthesis of luciferin-binding protein starts and increasing at the end of the night when synthesis of luciferin-binding protein stops. This suggests that it functions as a clock-controlled repressor, preventing the translation of lbp mRNA during the day.