A novel, poly(ethyl ethylene ether) inhibitor to trypsin was purified from marine cyanobacteria, Lyngbya confervoides from the coastal areas of Thalassery, North Kerala. The kinetics and the thermodynamic parameters of its interactions with the enzyme were also studied. It was demonstrated that the substrate binding, catalytic triad of the enzyme could be blocked by the inhibitor, as expressed by molecular simulation studies. The study also showed that the cyanobacterial group could prove to be a potential source of novel enzyme inhibitors for various applications.