Antibiotics are widely used in the treatment of human and animal diseases. Unreasonable use and abuse of antibiotics lead to the production and spread of resistant bacteria and resistance genes. Metagenomics can analyze the diversity of antibiotic resistance genes in different environments, and improve the existing or construct new metagenomic libraries, which will provide powerful references for future gene comparison. This article will review the application of metagenomics in the detection of microbial antibiotic resistance genes in humans, animals and the environment, and provide technical support for future assessment of resistance gene risks and addressing antibiotic resistance.