Drought stress is one of major environmental stresses in plants; this leads to reduce plant growth and crop yield. In this study, we selected fungal isolate for mitigating drought stress in pepper plants. To do this, 41 fungi were isolated from rhizosphere or bulk soils of various plants in Jeju, Gangneung, Hampyeong in Korea. Out of 41 isolates, we screened two isolates without phytotoxicity through seed germination of tomato, pepper, and cabbage treated with fungal spores; through following plant assay, we selected GL02 as a candidate for alleviating drought stress in pepper plants. As a result of greenhouse test of pepper plants in drought condition, the stomatal conductance on leaves of pepper plants treated with GL02 was increased, whereras the malondialdehyde (MDA) and electrolyte leakage were decreased compared to that in control plants. When stressed plants were rewatered, stomatal conductance of the plants treated with GL02 was increased; the electrolyte leakage was decreased. Based on internal transcribed spacer (ITS) sequencing analysis, isolate GL02 was belonging to genus Trichoderma. Taken together, drought stress in pepper plants treated with GL02 was alleviated, when it was rewatered after drought-stressed, the plants could be recovered effectively. Therefore, Trichoderma sp. GL02 could be used as a bio-fertilizer to alleviate drought stress in pepper plants.