The use of microalgae for the economic needs and the commercial goals determines the areas of the scientific researches that will make it possible to increase their productivity. It is also important to direct the metabolism of the algae to the activating of certain synthetic processes in order to obtain the desired compounds. The metals and non-metals, entering into the cell, have a high biochemical activity. These elements modify the metabolic reactions in general and the metabolic reactions related to the functioning of the genome of microalgae cells. Aim. The aim was to study the genetic polymorphism of Chlorella vulgaris under the action of such trace elements as selenium, zinc and chromium in order to optimize the methods of algae cultivation and the obtaining of the beneficial compounds. Methods. The hydrobiological methods of algae cultivation, DNA isolation method by Rogers S. and Bendich A. (1985), PCR-analysis with ISSR (inter simple sequence repeats)- and IRAP-markers (inter-retransposon amplified polymorphism) have been used. Results. For all samples of C. vulgaris 109 DNA-fragments were obtained and 42 of them were polymorphic (38.5%). Jacquard distances (DJ) between the samples of C. vulgaris culture (cultures are grown on the media with different elements compositions and control (standard conditions) were 0.232 (only selenite), 0.206 (selenite and zinc) and 0.300 (selenite and chromium). Conclusions. Probably the genetic modifications of C. vulgaris cells are caused by the additional introduction of the microelements into the culture medium. The genetic polymorphism of the algae grown on media with various trace elements and their combinations was like the genetic polymorphism of the unicellular green algae grown in the natural conditions. It indicates the absence of significant genotoxic effects of the trace elements and high metabolic and genetic plasticity of algal culture.