Recent findings showed that inhibition of the digestive enzyme trypsin by cyanobacterial metabolites can result in the death of the microcrustacean Daphnia. Compounds that are active against daphnid trypsin can therefore be considered as potentially toxic to Daphnia. Here we reported on the frequency of such compounds in the widely distributed cyanobacterial genus Planktothrix. Of the 89 Planktothrix strains analysed, about 70% produced inhibitors of daphnid trypsin. The strains tested positive represented three common Planktothrix species and were isolated from diverse localities and geographical regions. Our findings suggest therefore that inhibitors of daphnid trypsin are common in Planktothrix and maybe other cyanobacterial genera. These compounds should therefore be considered in future studies on the chemical ecology of cyanobacteria.