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With the increasing effects of global climate change and population growth, there is a high need for new agricultural practices to maximize efficiencies and reduce the efforts needed for developing new crop varieties that can withstand various abiotic stress. Plant-microbe association to optimize plant growth and increase plant host stress tolerance may play an essential role in improving environmental sustainability and economic viability, especially in the arid land habitats. In the present study, photosynthetic responsiveness was selected to demonstrate that a theromophilic endophytic (CpE) fungus isolated from the hot desert-adapted delile (Cullen plicata) roots can mediate heat stress tolerance in cucumber plants grown in the field during the summer season in Egypt. Initially, the CpE isolate was identified using an internal transcribed spacer, revealing 92% sequence homology with Thermomyces sp. Then the cucumber seeds were treated with CpE endophyte spore and allowed to grow in a growth chamber for three weeks before transplanting into the field station from May to July. The CpE treatment eliminates the adverse effects of heat stress on cucumber plants by maintaining the maximum quantum efficiency of photosystem II, photosynthesis rate, water use efficiency and increase root length relative to untreated plants. In addition, CpE treatments induced the significant accumulation of total sugars, flavonoids, saponins, soluble proteins and antioxidant enzyme activities in comparison with untreated cucumber plants. Our finding provides novel insights into the eco-physiological mechanisms of thermophilic CpE-mediated heat stress tolerance in cucumber, which signify the prospective applications of arid land-adapted endophytes in agricultural systems.