Protoberberinium salts, i.e. berberine (I), palmatine (II) and jatrorrhizine (III) prepared from Mahonia aquifolium (Pursh) Nutt. belong to isoquinoline alkaloids possessing interesting biological activity (e.g. antibacterial, antimalarial, antitumor). The characteristic UV/Vis absorption band maxima of I-III iodide salts were found in regions 350 and 425 nm in dimethylsulfoxide (DMSO) and ethanol solvents, and were only negligibly influenced by substitution changes on the C-2 and C-3 positions. The fluorescence intensity of protoberberinium salts monitored in ethanol solutions was significantly lowered by iodide counter-ions, and decreased in the order berberine > palmatine > jatrorrhizine. EPR spectroscopy supplied evidence of the formation of super-oxide anion radicals and singlet oxygen upon irradiation of berberine in oxygenated DMSO solvent. The photochemical generation of O(2) (.-) and (1)O(2) in DMSO solutions of palmatine and jatrorrhizine was substantially lower, and probably reflected the replacement of a photolabile methylenedioxy group at C-2 and C-3 positions in the berberine molecule by two methoxy groups in palmatine, and methoxyl (C-2) and hydroxyl (C-3) substitution in jatrorrhizine. Additionally, the powder EPR spectra of protoberberinium iodides I-III measured at 290 K revealed the presence of single-line EPR signals (g(eff) = 2.0044), which were attributed to hydroperoxidic structures produced by the autoxidation process. The photochemical reactions of protoberbenium salts producing reactive oxygen species after UVA excitation should be integrated in biological activity investigations, as well as in their applications in skin disorder treatment.