Endophytes are organisms that live between living plant cells and do not cause disease. Endophytes are ubiquitously present in diverse plant species, demonstrating a co-evolution with the plant host. Furthermore, different classes of microbial species, including bacteria, fungi, and actinomycetes colonize the internal plant tissues, leading to a wide range of implications. The medicinal plants associated with endophytes have been extensively studied as a potential source of bioactive compounds, with pharmacological attributes and biotechnological applications. Scientific breakthroughs in whole genome sequencing and annotation of endophyte-associated gene/metabolic pathways provided key insights into functional mechanisms and their dynamics within plants. Studies have highlighted the socio-economic implications of fungal endophytes in the environment, agriculture, and medicine with considerable success. Although extensively studied as a “production platform” of novel pharmacological metabolites, the molecular mechanisms of plant-endophyte dynamics remain less understood/explored for their efficient utilization in drug discovery and other biotechnological applications. This book aims to provide comprehensive knowledge about the multifaceted applications of endophytes.