Electron beam accelerators are reliable and durable equipments of produce ionizing radiation, and can be used industrially as a means to modify physical, chemical, or biological properties of commercial products. We used electron beam-induced mutagenesis to generate genetic diversity in the industrial strain of the microalgae Arthrospira platensis (A. platensis). A screen of A. platensis cells that were exposed to high energy (0.2 MeV, 1.2 mA) electron beams revealed 2 mutants, EM240 and EM384, that had increased levels of commercially valuable compounds compared to the parental strain of microalgae without the penalty to growth rate that is observed when other methods are used to increase these parameters. The increase in the levels of biologically active compounds, such as phycocyanin, lipids, phenolic compound, flavonoids and antioxidant enzymes (SOD and POD) in mutant cells resulted in enhanced antioxidant activity. Thus, to our knowledge, our study is the first to show that it is feasible to use electron-beam mutagenesis as a means to produce microalgae mutants that can be screened for high productivity of commercially valuable bioactive compounds for use in industrial processes.