Abstract: In recent years DNA fingerprinting technique was more and more popular in molecular biology researching. The DNA fingerprinting of bacterial fermentation microflora could directly reflect their differences on the DNA level. As a necessary part of the microbial fingerprinting,DNA fingerprinting of the modern molecular biology techniques had played an important role on the microbiological studies,and as well as in the field of identification,and genetic diversity researching of fermentation microflora. Usually DNA fingerprinting techniques such as RFLP,T-RFLP,SSCP,RAPD,DGGE,AFLP and so on have been applied in most fermentation microflora studies. Based on introduction of the common techniques of DNA fingerprinting technique and discussion of the application of DNA fingerprinting on the fermentation micoflora of cheese,the paper had combined the current situation of DNA fingerprinting on cheese,and introduced the principle,advantages and disadvantages,current researching situation of DNA fingerprinting techniques. And all of these discussions had important the practical significance and theoretical value to study the fermentation microflora of our traditional cheese.