The UV-protective ability of mucosporine-like amino acids (MAAs) has been well documented and is believed to serve as a protecting agent for Marine organisms from solar radiation. However, the effective UV absorption by MAAs has not been well correlated to MAA (neutral) structures. In this study, the origin of UV-ptotecting ability of MAAs was elucidated by experimental and theoretical spectroscopic investigations. The absorption maxima of mycosporine-glycine and shinorine in the UVA region Were practically unaffected over a wide range of pH 410 and only slightly blue-shifted at pH 1-2. It was revealed that the zwitterionic nature of the amino acid residue facilitates the protonation to the chromophoric 3-aminocyclohexenone and 1-amino-3-iminocyclohexene moieties and the operation of the charge resonance in the protonated species well accounts for their allowed low-energy transitions in the UVA region. The RI-CC2/TZVP calculations on model systems in their protonated forms well reproduced the observed transition energies and oscillator strengths of MAAs, only with insignificant systematic overestimations of the both values. The slight hypsochromic shifts at pH 1-2 were explained by (partial) protonation to a carboxylate anion in the amino acid residue, as confirmed by theory. Fluorescence spectral investigations of shinorine were also performed for the first time in water to confirm the effective nonradiative deactivation. Consequently, thiS study unequivocally demonstrated that the 3-aminocyclohexenone as well as 1-amino-3-iminocyclohexene moieties, which are readily protonated at a wide rang of pH, are responsible for the UV-protective ability of aqueous solution of MAAs.