This literature review explores the molecular mechanisms underlying plant-microbe interactions, focusing on key processes such as antibiosis, microbial signaling, endophytism, and transcriptional plasticity. It highlights the complex biochemical exchanges between plants and microorganisms, which influence plant physiology and have evolutionary implications. The review emphasizes the importance of understanding how plants distinguish between beneficial and antagonistic microorganisms, and it discusses the roles of transcription factors and epigenetic regulation in these interactions. The study also examines the impact of these interactions on plant health, disease resistance, and community structure. Additionally, it addresses the challenges and limitations in current research, including technical difficulties and the complexity of microbial communities. The review concludes by proposing new hypotheses and suggesting future research directions to enhance our understanding of plant-microbe interactions and their applications in biotechnology and sustainable agriculture.This literature review explores the molecular mechanisms underlying plant-microbe interactions, focusing on key processes such as antibiosis, microbial signaling, endophytism, and transcriptional plasticity. It highlights the complex biochemical exchanges between plants and microorganisms, which influence plant physiology and have evolutionary implications. The review emphasizes the importance of understanding how plants distinguish between beneficial and antagonistic microorganisms, and it discusses the roles of transcription factors and epigenetic regulation in these interactions. The study also examines the impact of these interactions on plant health, disease resistance, and community structure. Additionally, it addresses the challenges and limitations in current research, including technical difficulties and the complexity of microbial communities. The review concludes by proposing new hypotheses and suggesting future research directions to enhance our understanding of plant-microbe interactions and their applications in biotechnology and sustainable agriculture.