Abstract: Microbial molecular ecology is an interdisciplinary of molecular biology and microbial ecology. It is important to understand the composition and structure, function, the relationship between microorganisms and the relationship between microorganisms and the environment in microbial ecosystems. Microbial molecular ecology research techniques and methods widely used are comprehensively introduced, analyzed and summarized, and the advantages, disadvantages and applications of the techniques and methods are discussed. This study would provide a reference for understanding and regulating the kind and population of microbial communities in ecosystems.