In recent years, the increasingly frequent contact between humans and wild animals, coupled with the continuous mutation and evolution of pathogenic microorganisms, has led to a continuous increase and frequent outbreaks in emerging infectious diseases (EIDs), which has posed big threats and challenges to the global public health. On the occasion of the next outbreak of EIDs, it is hoped that the two major questions of ^"what is the pathogen^" and ^"where does the pathogen come from^" can be answered accurately and quickly through the rational use of relevant technical methods, so as to timely and effectively warn and control the outbreak of EIDs from the source. This article summarizes the pathogen identification and traceability analysis techniques of current emerging infectious diseases, and discusses the advantages and disadvantages of various technologies and their respective application fields.