Fluorescence spectroscopy is widely used to study water pollution. The fluorescence of water natural organic matter can be classified into two groups: the protein-like fluorescence originating from aromatic amino acids and the humic fluorescence originating from humic substances. Actually, the precise molecular origin of the protein-like fluorescence is unknown because this fluorescence may be caused by either free amino acids, peptides or proteins. Therefore, we studied the molecular origin of the protein-like fluorescence of Suwannee River natural organic matter and fractions A, B and C + D obtained by size exclusion chromatography/polyacrylamide gel electrophoresis. Fractions were analyzed by reversed-phase high-performance liquid chromatography. The electrophoretic mobilities of fractions varied in the order C + D > B > A and the molecular size in the opposite order. Our results show that the protein-like fluorescence is almost exclusively located in high molecular size fraction A and medium molecular size fraction B. Retention times and fluorescence emission spectra of authentic free aromatic amino acids tyrosine and tryptophan were identical with the retention times and emission spectra of several chromatographic peaks of fractions A and B. More than 50 % of the protein-like fluorescence is due to free aromatic amino acids incorporated in water natural organic matter.