Denaturing gradient gel electrophoresis (DGGE) is well-established molecular tools in microbial molecular ecology that allows the study of diversity and dynamics of microbial communities to be fast and easy to operate. It can describe microbial communities based on partial sequences of nucleic acid and monitor uncultured bacteria. Here, the basic principles of the technology were introduced and common issues in the analyses of microbial community by DGGE were discussed. Finally, the application and prospect of DGGE for understanding the diversity of wetland microbial communities were reviewed.