Microbes are important composition of ecology system. Nowadays it's very important to study the microbial diversity and community structure, especially in water bioremediation by microbiological resources. Modern molecular biology techniques provide effective methods to study the microbial ecosystem in aqua. Several techniques were summarized, including 16S rDNA clone library, DGGE (Denaturing gradient gel electrophoresis), RFLP (Restriction Fragment Length Polymorphism) and T-RFLP (Terminal Restriction Fragment Length Polymorphism), while their application to analyze water microbial diversity were introduced.