A novel strain SR–1.3 with algicidal properties and the ability to remove microcystin-LR was isolated from the water of Lake Sestroretskij Razliv during the active cyanobacteria vegetation. Based on the morphological and cultural characteristics and the results of sequencing of the ITS DNA region strain SR–1.3 was identified as Penicillium chrysogenum. The SR–1.3 strain exhibited algicidal activity against cyanobacteria and green algae. A dose-dependent and species-specific nature of the algicidal action of the P. chrysogenum SR–1.3 strain has been established. Cyanobacteria showed the highest sensitivity to strain SR–1.3. The complete lysis (100%) of cyanobacteria cells was observed when 10% (vol.) of the culture liquid or the micromycete filtrate were added to the medium. The algicidal effect of strain SR–1.3 on green algae was 30–70%, depending on the culture. According to the level of sensitivity to the algicidal effect SR–1.3, the test cultures can be arranged in the series Planktothrix agardhii Microcystis aeruginosa Aphanizomenon flos-aquae = Anabaena cylindrica Scenedesmus quadricauda Oocystis parva. The inhibitory effect of the strain SR-1.3 mycelium on the cyanobacteria and green algae growth did not exceed 3–6%. Based on the obtained results a conclusion was made about the indirect mechanism of the algicidal action of P. chrysogenum SR–1.3 by excretion into the medium of metabolites that inhibit and/or lyse cells of cyanobacteria and green algae. When toxigenic strains of M. aeruginosa and P. agardhii were cultivated on a medium containing exometabolites of strain SR–1.3, the concentrations of microcystins in the medium decreased by 3.3 and 1.8 times, respectively, compared with control variants. The ability of P. chrysogenum SR–1.3 to remove highly toxic microcystin-LR from the cultivation medium was revealed. The MC-LR content was found to decrease from 1.2 μg/ml to 0.79 μg/ml over 48 hours during the cultivation of strain SR–1.3 on medium with microcystin.