Cone photoreceptors in the murine retina are patterned by dorsal repression and ventral activation of S opsin. TR2, the nuclear thyroid hormone receptor  isoform 2, regulates dorsal repression. To determine the molecular mechanism by which TR2 acts, we compared the spatiotemporal expression of TR2 and S opsin from embryonic day (E) 13 through adulthood in C57BL/6 retinae. TR2 and S opsin are expressed in cone photoreceptors only. Both are transcribed by E13, and their levels increase with cone genesis. TR2 is expressed uniformly, but transiently, across the retina. mRNA levels are maximal by E17 at completion of cone genesis and again minimal before P5. S opsin is also transcribed by E13, but only in ventral cones. Repression in dorsal cones is established by E17, consistent with the occurrence of patterning during cone cell genesis. The uniform expression of TR2 suggests that repression of S opsin requires other dorsalspecific factors in addition to TR2. The mechanism by which TR2 functions was probed in transgenic animals with TR2 ablated, TR2 that is DNA binding defective, and TR2 that is ligand binding defective. These studies show that TR2 is necessary for dorsal repression, but not ventral activation of S opsin. TR2 must bind DNA and the ligand T3 (thyroid hormone) to repress S opsin. Once repression is established, T3 no longer regulates dorsal S opsin repression in adult animals. The transient, embryonic action of TR2 is consistent with a role (direct and/or indirect) in chromatin remodeling that leads to permanent gene silencing in terminally differentiated, dorsal cone photoreceptors.