Abstract: Blood borne pathogen infection often occurs in hospitalized patients with high mortality rate, the early and rapid identification of pathogens and appropriate antimicrobial treatment are the key measures to reduce the mortality. Blood culture is the gold standard in the diagnosis of blood borne pathogen infection, blood culture, however, is not only time-consuming but also non-sensitive with low positive rate. Molecular biology method can greatly reduce diagnosis time, improve the sensitivity and specificity of diagnosis and provide reliable evidence for the rational clinical drug use and accurate treatment, which can greatly improve the patient's survival rate. This paper summarizes the progress in the research of molecular biology methods for the diagnosis of blood-borne pathogens, including nucleic acid hybridization technique, nucleic acid amplification technique, fluorescence real-time quantitative PCR, DNA microarray and matrix assisted laser desorption/ionizaton time of flight mass spectrometry（MALDI-TOF-MS）.