Application of algicidal bacteria is a promising way in the control of harmful algal blooms. However, many environmental factors can strongly influence the algicidal efficiency of algicidal bacteria against harmful algae. Till now, the relationship between algicidal efficiency and environmental factors is still elusive. In order to explore the key factors which play important role in determining the algicidal efficiency of an algicidal bacterium Bacillus sp. B50 against Microcystis aeruginosa, the susceptibilities of thirteen M. aeruginosa strains to algicidal bacterium Bacillus sp. B50 were tested. The results indicated that these thirteen M. aeruginosa strains could be classified into three groups: high susceptive strains, moderate susceptive strains and, resistant ones. The susceptibility of these Microcystis strains to Bacillus sp. B50 did not correspond with microcystins-producing characteristics or cellular phenotype of M. aeruginosa. However, the susceptibility has a linear relationship with growth rate of these M. aeruginosa strains. Bacterial community in the culture of the resistant strains could modify the susceptibility of susceptive one to the stress from algicidal bacterium, but this modification could be diminished by enhancing inoculation density of algicidal bacterium. (C) 2014 Elsevier Ltd. All rights reserved.