Two bis-trifluoromethylated phenylretinal bacteriorhodopsin (bR) analogs were prepared and studied by F NMR and UV-vis spectroscopy. In contrast to those of visual pigments, only one fluorine signal was observed for the doubly labeled bR analogs. After considering different possible explanations, we believe the result probably reflects a more open hydrophobic pocket for the bR analogs allowing rapid equilibration (at the NMR scale) of the double labels. The extent of protein perturbation at the ortho position is different from that at the meta position.