The functional role of microcystins (MC) is poorly understood. Here, we investigated the effect of pure MC-LR recovered from the freshwater planktonic cyanobacterium Nostoc sp. BHU001 on five closely related cyanobacteria (Nostoc muscorum, Nostoc commune, Anabaena fertilissima, Anabaena doliolum, and Cylinderospermum majus) isolated from different habitats as well as on the producer itself (Nostoc sp. BHU001). MC-LR was found to be a general growth inhibitor active at nanomolar range (25-100 μg L −1 ). It inhibited the growth of all cyanobacterial strains in a concentration-dependent manner, except the producer. A. fertilissima was the most sensitive species. MC-LR affected vital metabolic processes such as photosynthesis, respiration, and nitrogen fixation. Nitrogenase activity showed maximum sensitivity, followed by respiration, photosynthesis, and general growth. The photosynthetic electron transport activity was maximally inhibited at PSI, followed by whole chain and PSII activities. Thus, MC-LR is active at multiple sites causing energy constraint to the vital metabolic processes of the target organisms. However, its requirement at high concentration, which is environmentally irrelevant, and lack of quantitative information on the extracellular release of MC-LR suggest that MC-LR has no allelopathic function and could be a part of a quantitative chemical defense system.