The magnitude and frequency of cyanobacteria blooms are increasing due to environmental changes including increased temperatures, eutrophication and anthropogenic inputs. Cyanobacteria are a source of diverse natural products that can negatively impact ecosystem and human health. The most commonly studied cyanopeptides are microcystins, a group of potent liver toxins and possible human carcinogens.Together with microcystins, common bloom forming cyanobacteria co-produce other cyanopeptide groups such as aeruginosins, anabaenopeptins, cyanobactins, cyanopeptolins, microginins and microviridins. There is a lack of toxicological and environmental concentration data for these lesser studied cyanopeptide groups.Advances in analytical techniques allow further comprehension of the complex metabolomes of cyanobacteria. Mass spectrometry-based metabolomic techniques can be applied to decipher the cyanopeptide profiles of common bloom-forming cyanobacterial strains. In this study, the cyanopeptide profiles of Planktothrix rubescens CPCC 507, P. agardhii CPCC 720, P. rubescens CPCC 731, P. rubescens CPCC 732, P. rubescens CPCC 733, and Oscillatoria tenuis CPCC 735 (possibly Planktothrix sp.) isolated from Ontario and Quebec lakes, were characterized using mass spectrometry-based metabolomics. Cyanopeptide chemical classes were determined based on shared structural features identified by characteristic product ions within their tandem mass spectra. Metabolomic strategies including multivariate analysis, diagnostic fragmentation filtering and global natural product society (GNPS) molecular networking were implemented to decipher strain-specific cyanopeptide profiles from metabolomic data sets. Two-hundred and twenty-five cyanopeptides were identified from the extracts of the six investigated strains. Each strain produced different mixtures of microcystins, aeruginosins, anabaenopeptins, cyanopeptolins and microviridins. Microginin and cyanobactin groups were not identified from studied strains. The most diverse cyanopeptide groups were cyanopeptolins and anabaenopeptins with eighty and sixty-one unique congeners, respectfully. This work provides critical information for the cyanopeptide composition present in Planktothrix extracts, consequently aiding in the prioritization of new natural products for isolation and risk characterizations. Furthermore, these complex mixtures of List of abbreviations: (HR)-MS/MS -high-resolution tandem mass spectrometry A/Ala -alanine AChE -acetylcholinesterase ACN -acetonitrile ACP -acyl carrier protein Adda -3-amino-9-methoxy-10-phenyl-2,6,8-trimethyldeca-4,6-dienoic acid AEG -N-2-aminoethyglycine Ahda -3-amino-2-hydroxy decanoic acid Ahoa -3-amino-2-hydroxy octanoic acid Ahp -3-amino-6-hydroxy-2-piperidone ALS/PDC -amyotrophic lateral sclerosis/Parkinsonism dementia complex ATXa -Anatoxin-a AP -anabaenopeptin AS -aeruginosin AT -acyltransferase ATX -anatoxin BAMA -β-amino-N-methylalanine BMAA -β-methylamino-alanine BW -body weight C/Cys -cysteine CB -cyanobactin cHAB -cyanobacterial harmful a...