Eichhornia crassipes is an invasive, floating macrophyte and may have biocontrol functions on harmful cyanobacteria blooms. Eichhornia produces N-phenyl-2-naphthylamine (PNA), a compound which can inhibit algae. However, the impact of PNA on allelopathic effects of the cyanobacterium Microcystis aeruginosa on other phytoplankton species is not clear. In this study, we tested whether PNA can influence the allelopathic effect of M. aeruginosa on the green alga Scenedesmus quadricauda. S. quadricauda was more sensitive to PNA than M. aeruginosa, with 72 h-EC50 values of 0.42 and 3.66 mg L−1, respectively. In addition, PNA significantly enhanced allelopathy by M. aeruginosa on S. quadricauda. Consequently, PNA had a greater impact on the green algae when Microcystis was present. In complex ecosystems with multiple species that release allelopathic substances, unintended interspecific interactions may occur, where allelopathy plays an important role under artificial or even natural contexts. It is hard to predict the competition outcomes among allelopathic organisms in these complex ecosystems, therefore a precautionary approach is required for biological control of algae.