Duckweed has been highlighted as an appropriate biomass for low-carbon industries because of its significantly high production rate and multiple resource value. However, the outbreak of microalgae is a practical issue that decreases duckweed production yield. This study demonstrated that the growth of the duckweed Lemna aequinoctialis from factory wastewater was enhanced by colonization with indigenous plant growth-promoting bacteria (PGPB), whereas the growth of a duckweed competitor microalga, Coelastrella sp. KC10, from the same wastewater was reduced by indigenous microalgal growth-inhibiting bacteria (MGIB). Finally, a quadruple co-culture of a synthetic duckweed holobiont, L. aequinoctialis colonized by both KLaR20 (PGPB) and KLaR16 (MGIB), and Coelastrella sp. KC10 successfully recovered the duckweed production level by 117.5% in frond number and 84.5% in dry weight compared to those in the absence of microalgae. This case study demonstrates for the first time that duckweed holobionts can be reconstructed and enforced to antagonize growth competitor microalgae.