Cyanobacteria were dominant from June to September in the Nakdong River and the Hoedong Reservoir. Microcystis aeruginosa was dominant from June to September; Anabaena flos-aquae from June to August and Aphanizomenon flos-aquae from July to August. Cyanobacterial neurotoxins, Anatoxin-a and saxitoxin were analyzed by electrospray ionization-mass spectrometry with strains of Aphanizomenon flos-aquae NIES-81 and Anabaena flosaquae NIER-10002. Anatoxin-a was not detected from the cultured Anabaena flos-aquae nor from the wild samples. Low levels of saxitoxin were detected in the cultured Aphanizomenon flos-aquae however, those of field samples were below the detection limit.