Abstract: The main shortages of traditional culture for identifying microbial phase in food are difficult to analysis dynamic changes of microorganisms at real time. In recent years, the advantages of polymerase chain reaction -denaturing gradient electrophoresis in revealing the changes of the microbial population are prominent. The principle, advantages and disadvantages of PCR-DGGE were introduced in this paper, the development and prospect of PCR-DGGE technology in food research and the microbial phase analysis were discussed either.