Anthocyanins are a class of natural compounds common in flowers and vegetables. Because of the increasing preference of consumers for food containing natural colorants and the demonstrated beneficial effects of anthocyanins on human health, it is important to decipher the molecular mechanisms of their action. Previous studies indicated that the anthocyanin cyanidin-3-glucoside (C3G) modulates the function of the photoreceptor rhodopsin. In this paper, we show using selective excitation 1H NMR spectroscopy that C3G binds to rhodopsin. Ligand resonances broaden upon rhodopsin addition and rhodopsin resonances exhibit chemical shift changes as well as broadening effects in specific resonances, in an activation state-dependent manner. Furthermore, dark-adapted and light-activated states of rhodopsin show preferences for different C3G species. Molecular docking studies of the flavylium cation, quinoidal base, carbinol pseudobase and chalcone forms of C3G to models of the dark, light-activated and opsin structures of rhodopsin also support this conclusion. The results provide new insights into anthocyanin–protein interactions and may have relevance for the enhancement of night vision by this class of compounds. This work is also the first report of the study of ligand binding to a full-length membrane receptor in detergent micelles by 1H NMR spectroscopy. Such studies were previously hampered by the presence of detergent micelle resonances, a problem overcome by the selective excitation approach.