Microbial culture-independent technology, such as DNA fingerprinting technology, pyrosequencing, molecular hybridization technology, metagenomics, metatranscriptomics, metaproteomics, metabolomics and so on, has developed rapidly and been applied extensively in many fields, which could assist in the identification of microbial species from natural or anthropogenic environment rapidly and accurately. The microbial culture-independent technology has provided crucial in-sights for revealing microbial community structures, functions and remediation mechanism during bioremediation process and improving the detection efficiency of bioremediation. This review is mainly focused on the advanced applications of molecular biology and microbial culture-independent technology of “-omics” in gauging microbial community structures, functions and dynamics at contaminated areas.