Siderophore is the iron-chelating agent excreted by microorganisms for acquisition of trace of iron. It has been reported that cyanobacteria also could utilize siderophores, but few structural properties of cyanobacterial siderophores were reported. We screened the siderophore producing activity for freshwater cyanobacterial species and found that Anabaena cylindrica (NIES-19) secreted two structural isomeric siderophores. Those structures were elucidated by FABMS analysis and 1H-1H, 1H-13C, and 1H-15N 2D NMR analyses.