A first-principles assisted study of the Raman spectrum associated with the photoactive chromophore in bacteriorhodopsin (bR) allowed the elucidation of the effective coupling existing between the π electrons of the retinylidene chromophore and the local environment of the Schiff base. The role of the counter-ion on the electronic and vibrational structure of the chromophore is investigated by means of density functional theory (DFT) calculations. Several molecular models of the retinylidene chromophore interacting with different counter-ions facing the Schiff base have been considered. The counter-ion induces a strong modulation of the position of both the UV–vis absorption maximum and the strong Raman active collective CC stretching mode, related to the effective conjugation coordinate (ECC). Experimental Raman and UV–vis absorption data are interpreted in the light of these theoretical findings. The data collected in this paper provide an interesting accumulation of points along the optical gap versus ECC wavenumber relationship. Copyright © 2011 John Wiley & Sons, Ltd.