There is a need to shift the absorbance of biomolecules to the optical transparency window of tissue for applications in optogenetics and photo-pharmacology. There are a few strategies to achieve the so-called red shift of the absorption maxima. Herein, a series of 11 merocyanine dyes were synthesized and employed as chromophores in place of retinal in bacteriorhodopsin (bR) to achieve a bathochromic shift of the absorption maxima relative to bR’s \({\lambda }_{\mathrm{max}}^{a}\) of 568 nm. Assembly with the apoprotein bacterioopsin (bO) led to stable, covalently bound chromoproteins with strongly bathochromic absorbance bands, except for three compounds. Maximal red shifts were observed for molecules 9, 2, and 8 in bR where the \({\lambda }_{\mathrm{max}}^{a}\) was 766, 755, and 736 nm, respectively. While these three merocyanines have different end groups, they share a similar structural feature, namely, a methyl group which is located at the retinal equivalent position 13 of the polyene chain. The absorption and fluorescence data are also presented for the retinal derivatives in their aldehyde, Schiff base (SB), and protonated SB (PSB) forms in solution. According to their hemicyanine character, the PSBs and their analogue bRs exhibited fluorescence quantum yields (Φ_f) several orders of magnitude greater than native bR (Φ_f 0.02 to 0.18 versus 1.5 × 10^–5 in bR) while also exhibiting much smaller Stokes shifts than bR (400 to 1000 cm⁻¹ versus 4030 cm⁻¹ in bR). The experimental results are complemented by quantum chemical calculations where excellent agreement between the experimental \({\lambda }_{\mathrm{max}}^{a}\)and the calculated \({\lambda }_{\mathrm{max}}^{a}\) was achieved with the second-order algebraic-diagrammatic construction [ADC(2)] method. In addition, quantum mechanics/molecular mechanics (QM/MM) calculations were employed to shed light on the origin of the bathochromic shift of merocyanine 2 in bR compared with native bR.