The role of anharmonic effects in the vibrational spectroscopy of the dark state and two major chromophore intermediates of the photoactive yellow protein (PYP) photocycle is examined via ab initio vibrational self-consistent field (VSCF) calculations and time-resolved resonance Raman spectroscopy. For the first time, anharmonicity is considered explicitly in calculating the vibrational spectra of an ensemble consisting of the PYP chromophore surrounded by model compounds used as mimics of the important active-site residues. Predictions of vibrational frequencies on an ab initio corrected semiempirical potential energy surface show remarkable agreement with experimental frequencies for all three states, thus shedding light on the potential along the reaction path. For example, calculated frequencies for vibrational modes of the red-shifted intermediate, PYPL, exhibit an overall average error of 0.82% from experiment. Upon analysis of anharmonicity patterns in the PYP modes we observe a decrease in anharmonicity in the C-8-C-9 stretching mode nu(29) (trans-cis isomerization marker mode) with the onset of the cis configuration in PYPL. This can be attributed to the loss of the hydrogen-bonding character of the adjacent C-9-O-2 to the methylamine (Cys69 backbone). For several of the modes, the anharmonicity is mostly due to mode-mode coupling, while for others it is mostly intrinsic. This study shows the importance of the inclusion of anharmonicity in theoretical spectroscopic calculations, and the sensitivity of experiments to anharmonicity. The characterization of protein active-site residues by small molecular mimics provides an acceptable chemical structural representation for biomolecular spectroscopy calculations.