Toxic cyanobacterial blooms are a threat because of secondary metabolite production. We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to identify intact microorganisms. Microgram quantities of prepared cells, including solvent (acetonitrile and ethanol) and alpha-cyano-4-hydroxycinnamic acid matrix, display spectra showing predominantly the secondary metabolites including known microcystins, micropeptin, and anabaenopeptolin. A new cyclic anabaenopeptolin has been identified using the Post-Source-Decay mode. Strains of various origins can easily be typed according to their cyclic peptide production, and toxic and nontoxic algal blooms can be differentiated within minutes.