Abstract: The rapid development of new technologies based on microbiomes and metagenomics provides unparalleled advantages in the discovery of novel microorganisms. Since the publication of concept of reverse etiology, it has played an increasingly important role in guiding the active prevention and control practice of emerging infectious diseases and has been widely used in the fields of public health and disease prevention and control. New metagenomics/metatranscriptomics technologies have further supported and facilitated reverse etiology research, and some progresses have been made in the development of theories, strategies and methodologies for assessing the pathogenic potentials of novel microorganisms. This paper summarizes the role, application of new metagenomics/metatranscriptomics technologies in reverse etilogy research and the challenges in its application for the purpose of improving the understanding of pathogens and theoretical and technical innovations.