Abstract: The microorganism detection, identification and genotyping are the most important aspects for the quality control in food and drug fields. However, the traditional microbial detection methods need relative long period and the result may be influenced greatly by subjective judgment of the researchers to some extent. And traditional methods have disadvantages in the discovering of new microorganisms or microorganisms that grow slowly. The development of modern identification and genotyping techniques provide new directions for the detection of microorganisms in food and drug field. In this review, the application of traditional and modern microorganism identification and genotyping techniques in the field of drug and food quality control is discussed. At the same time, it is aimed to propose new ideas in order to provide reference and technical guarantees for the development of new method for microorganism detection besides the aforementioned areas.