Photoactive yellow protein (PYP) is a bacterial photoreceptor containing a 4-hydroxycinnamyl chromophore. We report the resonance Raman spectra for the long-lived blue-shifted intermediate of PYP whose chromophore is isotopically labeled with C-13 at the carbonyl carbon atom or at the ring carbon atoms. Spectra have been also measured with PYP in D2O where the phenolic hydroxyl group of the chromophore is deuterated. All of the observed Raman bands are assigned on the basis of the observed isotope shifts and normal mode calculations using a density functional theory. The complete assignment provides a satisfactory framework for future investigations of the photocycle mechanism in PYP by vibrational spectroscopy.