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In this study, we attempted to synthesize visible light active nano-sized photocatalysts using metal oxides such as zinc oxide, zirconium oxide, tungsten oxide, and strontium titanium oxide with (MoCl₅)₂ as a dopant by the simple ball-milling method. Fourier-transform infrared spectroscopy data confirmed the presence of M-O-Mo linkage (M = Zn, Zr, W, and SrTi) in all the molybdenum-doped metal oxides (MoMOs), but only MoZnO inhibited the growth of the bloom-forming <i>Microcystis aeruginosa</i> under visible light in a concentration-dependent manner up to 10 mg/L. Further, structural characterization of MoZnO using FESEM and XRD exhibited the formation of typical hexagonal wurtzite nanocrystals of approximately 4 nm. Hydroxyl radical (·OH), reactive oxygen species (ROS), and lipid peroxidation assays revealed ·OH generated by MoZnO under the visible light seemed to cause peroxidation of the lipid membrane of <i>M. aeruginosa</i>, which led to an upsurge of intracellular ROS and consequently introduced the agglomeration of cyanobacteria. These results demonstrated that nano-sized MoZnO photocatalyst can be easily synthesized in a cost-effective ball-mill method and utilized for biological applications such as the reduction of harmful algal blooms. Further, our study implies that a simple ball-milling method can provide an easy, green, and scalable route for the synthesis of visible light active doped metal oxides.