Infectious　diseases　are　a　type　of　disease　caused　by　pathogenic　microorganisms.　Although　the　discovery　of　antibiotics　changed　the　treatment　of　infectious　diseases　and　reduced　the　mortality　of　bacterial　infections,　resistant　bacterial　strains　have　emerged.　Anti-infective　therapy　based　on　aetiological　evidence　is　the　gold　standard　for　clinical　treatment,　but　the　time　lag　and　low　positive　culture　rate　of　traditional　methods　of　pathogen　diagnosis　leads　to　relative　difficulty　in　obtaining　the　evidence　of　pathogens.　Compared　with　traditional　methods　of　pathogenic　diagnosis,　next-generation　and　third-generation　sequencing　technologies　have　many　advantages　in　the　detection　of　pathogenic　microorganisms.　In　this　review,　we　mainly　introduce　recent　progress　in　research　on　pathogenic　diagnostic　technology　and　the　applications　of　sequencing　technology　in　the　diagnosis　of　pathogenic　microorganisms.　This　review　provides　new　insights　into　the　application　of　sequencing　technology　in　the　clinical　diagnosis　of　microorganisms.　©　2019　The　Authors.　Journal　of　Cellular　and　Molecular　Medicine　published　by　John　Wiley　&　Sons　Ltd　and　Foundation　for　Cellular　and　Molecular　Medicine.