The paper presents the results of studies of the effect of multiwalled carbon nanotubes 18-20nm in concentrations of 1 and 10mg / ml for diatoms Pseudo-nitzschia pungens (clone PP-07) and golden alga Isochrysis galbana (clone TISO). The toxic effects of multiwalled nanotubes on both types of algae is revealed, which results in a decrease of the linear dimensions of cells, chloroplasts, and a reduced number of cells when incubated over 24h (Pseudo-nitzschia pungens) and 36hours (Isochrysis galbana).