Isotope-labeled riboflavin in DMSO was employed in conjunction with femtosecond time-resolved infrared vibrational spectroscopy and quantum chemical calculations to analyze and assign the electronically excited state vibrational modes of the isoalloxazine unit as a prototype for the cofactors in flavin binding blue-light receptors. Using the riboflavin (13)C-analogues RF-2-(13)C and RF-4,10a-(13)C, the carbonyl vibrations, in particular, were studied. Various quantum chemical models were applied that take into account a polarizable environment or the impact of hydrogen bonds. The CIS quantum-chemistry method was successfully applied to describe the lowest singlet excited electronic state in riboflavin. The experimentally observed frequencies and isotope-shifts as well as their variability in the diverse model calculations are discussed. On these grounds, a consistent assignment of the electronic ground and excited state vibrations is presented.