Freshwater cyanobacteria produce several bioactive secondary metabolites with diverse chemical structure, which may achieve high concentrations in the aquatic medium when cyanobacterial blooms occur. Some of the compounds released by cyanobacteria have allelopathic properties, influencing the biological processes of other phytoplankton or aquatic plants. These kinds of interactions are more easily detectable under laboratory studies; however their ecological relevance is often debated. Recent research has discovered new allelopathic properties in some cyanobacteria species, new allelochemicals and elucidated some of the allelopathic mechanisms. Ecosystem-level approaches have shed some light on the factors that influence allelopathic interactions, as well as how cyanobacteria may be able to modulate their surrounding environment by means of allelochemical release. Nevertheless, the role of allelopathy in cyanobacteria ecology is still not well understood, and its clarification should benefit from carefully designed field studies, chemical characterization of allelochemicals and new methodological approaches at the "omics" level.