In natural ecosystems, plants interact with a variety of microorganisms, forming intricate relationships that can influence plant health, growth, and responses to environmental challenges. These interactions include symbiotic, commensal, and pathogenic associations, with microbes such as bacteria, fungi, and actinomycetes playing diverse roles ranging from plant growth promotion to pathogen defense. Among these, endophytes are non-pathogenic microorganisms that reside within plant tissues, providing various benefits including enhanced resistance to environmental stress and pathogens. Research on endophytes focuses on understanding their diversity, ecological roles, and potential biotechnological applications. The diversity of endophyte communities varies by plant species, geographic location, and environmental conditions, and is typically studied using cultivation-dependent and independent techniques. Recent advances in multi-omics approaches, including metagenomics, metatranscriptomics, and metabolomics, have greatly enhanced our ability to investigate these communities. Additionally, the evolution of endophyte-plant interactions, shaped by vertical and horizontal transmission, reflects the complexity of symbiotic relationships that have developed over time. This chapter explores the dynamics of plant-endophyte interactions, the diversity of endophytes across different plant compartments, and the cutting-edge techniques used to identify and study endophyte communities, highlighting their significance in improving plant health and resilience.