Metagenomics uses direct sequencing of clinical specimens without culturing, and bioinformatics techniques to identify and characterize microorganisms, including DNA/RNA viruses, bacteria, fungi, protozoans, and helminth viruses and bacteria. By determining the entire genomic sequence of a pathogen, scientists and clinicians can decipher not just the organism, but also strain type, which informs transmission patterns and identifies sequences known to be antimicrobial resistance (AMR) markers. AMR markers inform treatment options by indicating which antivirals or antibiotics will not be effective against the target pathogen. Moreover, metagenomics allows the detection of co-infections that, eg. can be the cause of death in many COVID-19 patients. In this presentation, the implementation of metagenomics in clinical microbiology will be discussed, and examples of its use in real life will be presented.