Effect of several endophytic bacterial strains of Bacillus subtilis on growth of Scenedesmus quadricauda and Chlorella vulgaris algae was investigated. Introduction of bacillus strains into the algal cultures diminished the cell number of microalgae. The cells of C. vulgaris exhibited equal sensitivity to all the endophyte strains examined. The number of S. quadricaudas cells reduced to larger extent by the 7th day of algal culturing in the presence of B. subtilis 11V or 11VM strains than in the presence of B. subtilis 26D strain, the latter strain being the main component of the commercial biofungicide Fitosporin-M. Washed bacterial cells inactivated by autoclaving did not reduce the number of C. vulgaris cells. The bacterial cells that were autoclaved without separation from the culture liquid, as well as the autoclaved supernatant of cell suspension exerted the same inhibitory effect as living bacterial cells. The decrease in the algal cell number under the action of endophytic bacillus strains is presumably due to thermostable biologically active substances synthesized and secreted by the bacillus strains.