Metagenomics (metagenome) obtained all the microorganisms genome in specific biological environment from DNA samples directly from soil,water and skin,body cavity of human and animals. The metagenomic library was constructed by cloning them into alternative host cells using the vector,which is a discipline of screening new active substances and new genes by high-throughput sequencing. Therefore,using metagenomics not only can effectively detect the composition of microbial community of specific environment,but also greatly expanded the utilize the space of the microbial resources,developed of the next sequencing, enriched the content of bioinformatics. Based on the advantages of metagenomics,we summarized the major advances of metagenomics in human and animal pathogenic microorganisms in recent years,which might be used for the investigation and analysis of microbial pathogens of laboratory animal, animal epidemic monitoring and diagnosis of biological safety.