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In recent years, drought has become one of the most widespread global problems as a result of drastic climate change all over the world. In order to increase the efficiency of cultivation of agricultural crops under the conditions of drought, research was conducted aimed at determining the diversity of endophytic microorganisms of xerophytic and halophytic plants grown under the influence of this stress factor and evaluating their characteristics and potential is of great importance. This article describes the results of the research aimed at isolating, identifying and evaluating some properties of endophytic bacteria from Peganum harmala L., which is widespread in arid regions of Uzbekistan. These data are being published for the first time in terms of area and vegetation. The results of studying P. harmala endophytic bacteria diversity, species composition, resistance to pathogenic fungi confirm that this plant is a potential source of promising endophytic bacteria. In the experiments, 24 promising isotypes of endophytic bacteria were isolated from P. harmala, which were the research objects. Five strains were selected by evaluating the colonization potential of the isolated isolates under drought conditions and resistance of the selected strains to pathogenic fungi was evaluated. These promising strains were identified using molecular genetic methods.