<jats:p> <jats:italic>Microcystis</jats:italic> sp. has been recognized in recent years as a producer of a high number of secondary metabolites. Among these, peptides that are produced by the non-ribosomal peptide synthetase pathway often show bioactivity or are toxic to humans. The production of particular peptides is specific for individual <jats:italic>Microcystis</jats:italic> clones, allowing their characterization as chemotypes by analysing the peptidome. The authors studied the <jats:italic>in situ</jats:italic> diversity of peptides and chemotypes in <jats:italic>Microcystis</jats:italic> communities from lakes in and around Berlin, Germany, by direct analysis of individual colonies by MALDI-TOF mass spectrometry. From 165 colonies analysed a total of 46 individual peptides could be identified, 21 of which have not been described previously. For six of the new peptides the structures could be elucidated from fragment patterns, while for others only a preliminary classification could be achieved. In most colonies, two to ten individual peptides were detected. In 19 colonies, 16 of which were identified as <jats:italic>M. wesenbergii</jats:italic>, no peptide metabolites could be detected. The peptide data of 146 colonies were subjected to an ordination (principal components analysis). The principal components were clearly formed by the microcystin variants Mcyst-LR, -RR and -YR, anabaenopeptins B and E/F, a putative microviridin, and a new cyanopeptolin. In the resulting ordination plots most colonies were grouped into five distinct groups, while 40 colonies scattered widely outside these groups. In some cases colonies from different lakes clustered closely, indicating the presence of similar chemotypes in the respective samples. With respect to colony morphology no clear correlation between a chemotype and a morphospecies could be established, but <jats:italic>M. aeruginosa</jats:italic>, for example, was found to produce predominantly microcystins. In contrast, <jats:italic>M. ichthyoblabe</jats:italic> colonies were mostly negative for microcystins and instead produced anabaenopeptins. The number of peptides detected in a limited number of samples and the various combinations of peptides in individual <jats:italic>Microcystis</jats:italic> colonies highlights the immense metabolic potential and diversity of this genus.