In plant species, fungal endophytes are common and live in living tissues like leaves, stems, branches, and roots without causing any symptoms. Endophytes and their host plants have complicated connections that can range from mutualistic to harmful. Beneficial endophytes have the ability to improve plant fitness, which has raised attention in their possible uses in integrated plant health management. Fungal endophytes play important roles in plant defensive system, which is also elaborated in this chapter, with a focus on defense against non-insect pests like nematodes, bacteria, viruses, mites, and fungi. We look at the strategies endophytes use to combat these pests and emphasize the importance of these fungi in both present and future farming methods. We also offer a comprehensive list of endophytes that are beneficial to plants, including information on their typical habitats and uses in different research projects. This review is a thorough resource for learning about endophytes’ potential in extensive agricultural applications. Fungal endophytes and plants have symbiotic connections in natural ecosystems, impacting plant populations through lower water consumption, higher biomass, and improved stress tolerance. Even after more than a century of study, little is known about the ecological significance of endophytes. Based on phylogenetic and life history characteristics, endophytes have traditionally been divided into two groups: clavicipitaceous (C) and nonclavicipitaceous (NC). According to our data, NC-endophytes are classified into three different functional groups that are distinguished by their capacity for host colonization, transmission, biodiversity, and fitness benefits. We suggest important areas for future endophyte biology research by comparing the life histories, host relationships, and ecophysiological roles of C- and NC-endophytes using this framework.