Assignments are provided of prominent features in the recently measured Fourier transform infrared (FTIR) difference spect ra of green fluorescent and photoactive yellow proteins (GFP, PYP) employing ab initio calculations of the ground electronic state structures and vibrational spectra of their chromophores in selected protonation states. Particular attention is addressed to inferring the protonation states of wild-type GFP chromophore and to reconciling the measured FTIR difference spectrum with a proposed proton shuttle mechanism in which protonated and deprotonated forms of the chromophore are paired with corresponding charge states of a Glu222 residue shuttle terminus. The calculated GFP IR difference spectrum obtained from the neutral-anionic pair of chromophores is found to be in general accord with the FTIR measurements on wild-type GFP in its protonated and deprotonated farms, whereas the spectrum obtained from the zwitterionic-cationic pair of chromophores provides a less satisfactory simulation of the data. The apparent absence of a carbonyl band in the measured GFP FTIR difference spectrum, a feature expected upon protonation of the carboxylic Glu222 residue, is reconciled by the presence of a carbonyl mode in the imidazole ring of the neutral chromophore which partially obscures the anticipated R-COOH Glu222 feature in the calculated spectrum. By contrast, the corresponding carbonyl mode in the PYP chromophore is predicted to be significantly weaker and at lower frequency than in GFP, accounting in part for the presence of an unobscured prominent R-COOH Glu46. residue carbonyl mode in the measured PYP FTIR difference spectrum. Accordingly, the present ab initio theoretical study supports the predominance of neutral and anionic forms of wild-type GFP chromophore, and it argueably reconciles the available FTIR data with a probable Glu222 terminus of the proposed proton shuttle mechanism in the protein. Additional experimental studies of IR and Raman difference spectra in GFP and PYP, including particularly isotopic substitutions, are suggested to complement additional theoretical studies in progress.