Endophytic fungi are microorganisms that live symbiotically in healthy plant tissues for all or part of their life cycle without causing disease. They exhibit high biological diversity and have been found in a wide range of plant groups, including both vascular and nonvascular plants. Isolating and identifying endophytic fungi is crucial for studying the evolutionary relationship between plants and fungi. Alongside morphological identification, molecular phylogeny methods are essential for accurately determining fungal species. The ITS region is a crucial molecular marker with a high accuracy rate for identification. Endophytic fungi can enhance plant performance through various mechanisms, including promoting growth, nutrient uptake, and stress tolerance, such as drought and salinity. Fungi play a crucial role in enhancing plant health by promoting growth and increasing resistance to pathogens, insects, and herbivores through the production of secondary metabolites and induction of phytoalexins. These fungi are being explored as a promising source of bioactive compounds with various applications in the pharmaceuticals, food, and agriculture industries.