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In the current work, a comparative study of the influence of space flight conditions and model experiments on the photosynthetic apparatus of cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis) was presented. The cell culture of the wild-type Synechocystis launched into space on the satellite “Foton M4”, and it orbited the Earth for 45 days. For modelling conditions of the space flight, cyclotron U-120 SINP MSU was used, which yields accelerated helium nuclei with an energy of about 30.3 MeV. Changes in the structural and functional state of the photosynthetic membranes of cyanobacteria were obtained by a variety of optical methods, including fluorescence spectroscopy with picosecond time resolution, and modelling the thylakoid membranes. Phycobilisomes decouple from the photosystems under exposure to ionizing radiation. A possible radioprotective role of the phycobilisomes was revealed. After space flight or exposure to high doses of ionizing radiation, the cells of Synechocystis sp. remained capable of autotrophic growth and were able to restore cell culture with spectral and functional characteristics indistinguishable from control samples. The cell culture of Synechocystis sp., which returned to Earth after space flight, was included in the collection of microorganisms of the Faculty of Biology, Lomonosov Moscow State University.