Toxic water blooms from cyanobacteria in lakes and rivers are a worldwide phenomenon. A new technique is presented for the rapid detection of toxic and nontoxic blooms. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) was employed to identify mainly peptide metabolites (microcystins, anabaenopeptins, cyanopeptolins, microviridins, microginins and aeruginosins) from microgram quantities of prepared cells within minutes. The spectra show the presence of peptides in strains or water blooms simultaneously. A new compound has been identified using the post source decay (PSD) and collision induced dissociation (CID) mode. This new compound has been defined as anabaenoeptin G. The potential of the method for screening of various secondary metabolite producers for defined products including antibiotics is discussed.