Abstract: It is difficult to cultivate all flora in animal gastrointestinal tract by using traditional methods, so it is difficult to identify the difference of animal gastrointestinal microbes in each stage. Denaturing gradient gel electrophoresis （DGGE） can avoid the disadvantages of traditional methods and can confirm the difference in animal gastrointestinal microbiota system and the diversity of flora. The basic principle, advantages and disadvantages of DGGE and its application in animal gastrointestinal microbiota system were mainly summarized in this paper.