Abstract: Rapid detection of pathogenic microorganisms was the key way to prevent and control of foodborne diseases. Because traditional microbiological detection methods were cumbersome and low sensitivity, they failed to meet the needs of rapid detection. Using modern molecular biological detection methods, pathogenic microorganisms can be quickly detected and the relationship between pathogenic bacteria can be determined as well. To trace the source of disease, many technologies, such as polymerase chain reaction (PCR) technology, digital PCR technology, etc., can improve the specificity and sensitivity of the detection. However, higher requirements for the experimental apparatus and the detection efficiency are usually accompanied with disadvantages. Quantitative tandem repeat analysis, random amplified polymorphic DNA technology, genotyping and other technologies can quickly type microbial molecules and save detection time, but the operation is cumbersome and requires high-quality laboratory personnel; enzyme-linked immunosorbent assay, immunomagnetic separation and immunomagnetic beads combined with PCR can specifically identify pathogens and can quickly isolate target microorganisms, but the cost is high. This review summarizes the progress of PCR based molecular biological detection methods, molecular typing methods and immunological detection methods in order to provide reference for the technical development of microbial detection methods.