Allelopathy has been applied to control nuisance algae in aquatic systems, but the effects of allelochemicals on the broad spectrum of algae are not well understood. We investigate algicidal effects of the allelochemical juglone on the bloom-forming, harmful algae Microcystis aeruginosa and Stephanodiscus hantzschii, and on several non-target algal species including cyanobacteria (Anabaena flos–aquae, Oscillatoria curviceps, and Phormidium subfuscum), diatoms (Asterionella formosa, Fragilaria crotonensis, and Synedra acus), and green algae (Chlorella vulgaris, Scenedesmus ecornis, and Scenedesmus quadricauda), in laboratory and field enclosure bioassays. Under three treatment concentrations (0.01, 0.1, and 1 mg L−1) of juglone, Microcystis cell density is significantly reduced by 35–93%. Concentrations of 0.1 and 1 mg L−1 inhibits Stephanodiscus growth almost equally (66% and 75%, respectively). To contrast, juglone produces a stimulatory allelopathic effect on three green algae, and other tested diatoms showed hormesis. Overall, the cyanobacteria are more sensitive to juglone than the green algae and diatoms. These results indicate that the allelopathic effects of juglone on microalgae vary depending on their characteristic cellular morphology and anatomy.