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The viability and ultrastructure of spores of seven strains of microscopic fungi were investigated after 961 days of exposure in outer space on the external surface of the International Space Station. The physical exposure conditions were as follows: cosmic radiation, 750 mGy; minimum temperature, −7°C; maximum temperature, 87.5°C; average temperature, 20.6°C; space vacuum, from 10–7 to 10–4 Pa; solar ultraviolet radiation was shielded by the equipment. Spores of most of the studied strains survived after such prolonged exposure in outer space. The spores exposed in space had a higher viability rate than spores stored for the same period under laboratory conditions, as evidenced by the data on germination percentages and colony numbers on nutrient media. The highest germination percentages were observed for spores of Aspergillus piperis and Alternaria alternata. The survival level of spores of these strains exceeded 60% in the experimental samples; however, it was almost threefold and eightfold lower in the “terrestrial” control for A. piperis and A. alternata, respectively. Presumably, dehydration of spores in the space vacuum did not disrupt their integrity but, on the contrary, contributed to their long-term preservation. All ultrathin sections of spores were characterized by the presence of cells with impaired integrity. Prolonged storage of spores of Aspergillus ochraceus and A. alternata under laboratory and space conditions in many cases caused destruction of their cell wall, which partly explained the observed differences in viability. The obtained data allow the possibility of transfer of fungal spores to other celestial bodies and in the reverse direction to Earth, which should be taken into account when planning automated missions to other planets, primarily to Mars.