After chemical reduction of the retinylidene-lysine Schiff base linkage in bacteriorhodopsin, the retinyl residue is covalently attached to Lys-216 (with a possible minor fraction on Lys-172) or to both Lys-216(172) and Lys-40/41. The linkage site (up to 100% on Lys-216; up to 70% on Lys-40/41) depends on whether the sample is reduced in the light or dark, whether the sample is light or dark adapted, and on temperature. Absorbance and circular dichroism spectra indicate that the retinyl residue is in its original binding site after reduction in the light. Thus, the different attachment sites may reflect changes that occur during the photoreaction cycle or during light/dark adaptation, or the reduction of accidental physiologically irrelevant Schiff base linkages to lysines close to the normal linkage in the structure of bacteriorhodopsin. In either case, the retinal does not leave its binding site. This last point severely limits the possible arrangements of the amino acid sequence in the bacteriorhodopsin tertiary structure and clearly distinguishes two models that are consistent with all criteria.