Autophagy plays a direct or indirect roles in plant growth and development, pathogen invasion and immunity. It is involved in the control of cell homeostasis and modulates plant response and adaptation to various abiotic stress stimuli. The formation and motility of autophagosomes require microtubule dynamics. The manner in which autophagy can be induced by microgravity in plants has not been previously studied. Investigating how plants can cope with the absence of gravity is a critical task in space biology, since growing plants as a food source on the space station is in particular demand for the future. The present study demonstrates and confirms that microgravity affects the growth and development of plants. Using different GFP-expressing Arabidopsis thaliana lines (GFP-ATG8 and GFP-MAP4), laser scanning confocal microscopy and gene expression analysis of 6 α-tubulin (tua), 9 β-tubulin (tub) and 9 atg8 genes, we can conclude that main microgravity-induced stress response in plants is observed during the first 6-9 days of the microgravity experiments. It is shown that the morphological changes found in plants are directly related to changes in the organization and dynamics of microtubules. It was found that in root cells microtubules become disorganized after 6 days of growing plants under microgravity conditions, which leads to visible morphological changes in the plants. However, after 9-12 days of the experiment no dramatic disturbances in the orientation and organization of MTs were identified. The results obtained using LysoTracker™ Red and A. thaliana transgenic line (GFP-ATG8a) in both cases showed induction of autophagy and maximum level of autophagosome formation in plant root cells after 6 days of plant growth, and then a gradual decrease of autophagosomes in the same cells after 9 and 12 days under microgravity. The results of transcriptome analysis of tubulin and atg8 genes reveal connection between development of autophagy and functioning of microtubules. In particular, the most pronounced increase of expression in response to microgravity exposure was observed of tua2, tua3, tub2, tub3 and atg8i genes. It should be noted that the main responses to stress were established after 6-9 days of exposure to microgravitation, while after 12 days of the experiment, an adaptive response of plants to microgravity-induced stress was observed. The findings provide a basis for further studies of cellular mechanisms of autophagy and their interaction with cytoskeletal structures, in particular microtubules, to enhance plant adaptation to microgravity conditions