Cyanobacteria are recognized as producers of a broad variety of bioactive metabolites. Among these, the peptides synthesized by the non-ribosomal peptide synthetase pathway occur in high structural variability. One class of cyanobacterial peptides, the cyanopeptolins or micropeptins, have been shown to be strong inhibitors of vertebrate serine proteases, like trypsin. In the present study we screened extracts of ten strains of the unicellular cyanobacterium Microcystis sp. for their potential to inhibit trypsin-like activity in the planktonic crustacea Daphnia, the main herbivores in freshwater ecosystem. Respective standardized IC50's varied for nearly two orders of magnitude. In HPLC fractions we could identify mainly cyanopeptolins as active compounds by MALDI-TOF mass spectrometry. Cyanopeptolins were found in 22 structural variants with 13 variants produced by one strain alone. Peptides of the microviridin class were moderately active while no activity was evident for microginins and microcystins. Among the cyanopeptolins only those were active that had an arginine or lysine residue N-terminal to the modified amino acid 3-amino-6-hydroxy-piperidone. Structural variants that had a tyrosine residue at this particular position did not inhibit trypsin-like activity. The highly variable composition of the side chain of cyanopeptolins had no marked effect on the activity. Among the six cyanobacterial strains we tested intensively two did not produce any cyanopeptolins and were accordingly less active as crude extracts. The present study underlines the potential importance of the biochemistry of cyanobacteria for the feeding ecology of a planktonic herbivore.