Mitigation of harmful cyanobacterial blooms that constitute a serious threat to water quality, particularly in eutrophic water, such as in aquaculture, is essential. Thus, in this study, we tested the efficacy of selected cyanocides towards bloom control in laboratory and outdoor mesocosm experiments. Specifically, we focused on the applicability of a group of cationic disinfectants, alkyltrimethyl ammonium (ATMA) compounds and H2O2. The biocidal effect of four ATMA cations with different alkyl chain lengths was evaluated ex situ using Microcystis colonies collected from a fish pond. The most effective compound, octadecyl trimethyl ammonium (ODTMA), was further evaluated for its selectivity towards 24 cyanobacteria and eukaryotic algae species, including Cyanobacteria, Chlorophyta, Bacillariophyta, Euglenozoa and Cryptophyta. The results indicated selective inhibition of cyanobacteria by ODTMA-Br (C18) on both Chroccocales and Nostocales, but a minor effect on Chlorophytes and Bacillariophytes. The efficacy of ODTMA-Br (C18) (6.4 mu M) in mitigating the Microcystis population was compared with that of a single low dose of H2O2 treatments (117.6 mu M). ODTMA-Br (C18) suppressed the regrowth of Microcystis for a longer duration than did H2O2. The results suggested that ODTMA-Br (C18) may be used as an effective cyanocide and that it is worth further evaluating this group of cationic compounds as a treatment to mitigate cyanobacterial blooms in aquaculture.