Wetland ecosystem has important environmental and ecological functions in material circulation, energy flow and pollutant degradation. In recent years, climate change, salinization and human activities posed serious threats to the health of wetland ecosystem. Microorganism as an important part of wetland ecosystem plays a vital role in material circulation, energy flow, fertility formation and pollutant degradation. This article summarized the traditional and molecular research methods of wetland soil microbe, and presented the future research directions, so as to offer some support for the application of microbial diversity analyzing methods on wetland soil microbe.