Allelopathic effects are one of the factors potentially influencing the succession ofphytoplankton communities; however, their influence has often been neglected.This is especially true for cyanobacteria that often outcompete other phytoplanktonspecies and form blooms causing severe problems. Allelopathic effects ofcyanobacteria can play an important role for phytoplankton succession. In thischapter, we introduce the different ways how aquatic organisms are influenced bycyanobacterial allelochemicals; the mechanisms of their interaction from the aspects of chemical intermediates, target reaction, and target signals; and interferingfactors and the ecological consequences of this process.Cyanobacteria produce and excrete a variety of allelopathic compounds thataffect other Cyanophyta, eukaryotic algae, bacteria, zooplankton, higher plants,and fish and mammalian cells. These effects are regulated by various abiotic andbiotic conditions, such as nutrient availability, temperature, and light intensity butalso cell density and growth phase of the source cyanobacterial community. Thebioactive metabolites include cyclic peptides, alkaloids, terpenoids, and otherswhich can have a variety of inhibitory effects on the different target organisms.Ecological consequences such as declines in biodiversity and accumulation oftoxins in the food chain have been shown. However, most of these compoundshave not yet been fully tested regarding their full range of effects on naturalphytoplankton communities. A detailed elucidation of the influence ofcyanobacterial allelochemicals is of key importance for understanding and managingthe succession of natural phytoplankton communities