Microcystins generated by Microcystis aeruginosa are commonly detected in freshwater bodies and their removal becomes an emerging field recently owing to the toxicity. Here we report the structural characterization of degradation products from the photocatalysis of microcystin-LR (MC-LR). To achieve efficient photocatalytic degradation of MC-LR, we fabricated highly ordered TiO2 nanotubes using anodization method. The surface morphology of TiO2 nanotubes depends primarily on the anodic voltage and the optimum value is 20V. Under UV irradiation, the concentration of MC-LR decreases by 84.6% when using TiO2 nanotubes anodized at 20 V within 30 min. The degradation intermediates of MC-LR are detected with mass spectrometry (MS) and seven main intermediates are observed in liquid chromatography mass spectrometry (LC/MS) chromatogram. We propose the possible structures of the intermediates of MC-LR and infer its possible degradation pathways. The results indicate that the conjugated double bond and methoxy group in the Adda chain, as well as the conjugated system in the Mdha amino acid, are susceptible to be initially attacked by hydroxyl radicals. In addition, it is deduced that the peptides undergo breakdown from Mdha, then their carboxyl and amino groups are stepwise hydrolyzed and the side chain of the amino acid is oxidized. (C) 2013 Elsevier B.V. All rights reserved.