Eutrophication is a major management issue in shallow lakes worldwide. The role of allelopathy in aquatic systems has received increasing attention as a potential means of controlling algal blooms. Macrophytes with allelopathic potential may play an important role in the restoration of eutrophic lakes. Our objective was to investigate the allelopathic effect of the freshwater stonewort, Chara australis, and the submerged angiosperm, Potamogeton crispus, on microalgae. To detect possible allelopathic effects, we compared the growth of a cyanobacterial species, Anabaena variabilis and a green alga, Scenedesmus quadricauda, in the presence and absence of macrophyte extracts, exudates and live material. We found a significant negative effect of all treatments on A. variabilis, with the strongest effect produced by C. australis. In contrast, no effect of macrophyte extracts was evident on the growth of S. quadricauda. This absence of effect confirmed earlier findings that macrophyte allelochemicals are specific to particular target organisms. Our results suggest that allelopathic macrophytes have the potential to mitigate phytoplankton blooms in systems dominated by A. variabilis and perhaps other cyanobacteria.