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Microcystis aeruginosa (M. aeruginosa), as the dominant algae in eutrophic water bodies, has caused a serious harm to the local eco-environment. A biological tool, employing allelopathic inhibitory of eucalyptus to control M. aeruginosa, has been receiving tremendous attention. This work presents the results of the allelopathic inhibitory effects of eucalyptus (Eucalyptus grandis x E.urophylla 'GLGU9') extracts of roots (ERE), stems (ESE), and leaves (ELE) on culture solutions of M. aeruginosa and its ecophysiological mechanism. The inhibitory effects of the extracts on the growth of M. aeruginosa varied greatly with ELE exhibiting the highest level of potency. Modes of action by which ELE inhibited M. aeruginosa growth were established. They involved reduction in photosynthesis, disruption of the cell membrane integrity, and inhibition of esterase activities of the cyanobacterial cells. However, ELE did not exhibit any gradients of toxicity towards zebrafish nor Washington grass plant. Species abundance and diversity in the systems remained likewise unaffected by ELE. The synergistic interaction between ELE and single-component allelochemicals (e.g., gallic acid and berberine) was ascribed to the increase in efficacy of allelochemicals in the various systems. The results of this study provide an underlying, novel, and attractive approach for controlling the growth of M. aeruginosa in aquatic environments. (C) 2019 Elsevier Ltd. All rights reserved.