Chromophoric water-soluble organic matter in atmospheric aerosols potentially plays an important role in aqueous reactions and light absorption by organics. The fluorescence and chemical-structural characteristics of the chromophoric water-soluble organic matter in submicron aerosols collected in urban, forest, and marine environments (Nagoya, Kii Peninsula, and the tropical Eastern Pacific) were investigated using excitation-emission matrices (EEMs) and a high-resolution aerosol mass spectrometer. A total of three types of water-soluble chromophores, two with fluorescence characteristics similar to those of humiclike substances (HULIS-1 and HULIS-2) and one with fluorescence characteristics similar to those of protein compounds (PLOM), were identified in atmospheric aerosols by parallel factor analysis (PARAFAC) for EEMs. We found that the chromophore components of HULIS-1 and -2 were associated with highly and less-oxygenated structures, respectively, which may provide a clue to understanding the chemical formation or loss of organic chromophores in atmospheric aerosols. Whereas HULIS-1 was ubiquitous in water-soluble chromophores over different environments, HULIS-2 was abundant only in terrestrial aerosols, and PLOM was abundant in marine aerosols. These findings are useful for further studies regarding the classification and source identification of chromophores in atmospheric aerosols.