Bacterial strain B-9 possesses hydrolytic enzymes capable of degrading microcystins (MCs) and nodularin that are toxic cyclic peptides produced by cyanobacteria. In the present study, the degradation activities of the cell extract of B-9 against non-toxic cyanobacterial cyclic peptides other than the MCs and nodularin were investigated, and the degradation products were analyzed by liquid chromatography/ion trap tandem mass spectrometry (LC/ITMS). It was confirmed that B-9 could also degrade these cyanobacterial cyclic peptides by hydrolysis of their peptide bonds. These results indicated that this bacterium possesses a very unique hydrolytic activity that can degrade structurally different cyclic peptides and that this may be effective for the detoxification of hazardous cyclic peptides.