Environmental bioremediation technologies are undoubtedly more economical and environmental friendly, and present a good application prospect. Microorganisms can be used to monitor environmental changes for their quickly respond to environmental changes. Microbiological molecular biology methods have attracted more and more attention from human beings, and their applications in the environment is also expanding. Genomics, transcriptomics, proteomics, and metabolomics are four major molecular biology techniques. This review summarizes application of molecular biological methods in environmental engineering in 2017. The summary includes methods for DNA, RNA, and protein extraction, the application of four major technologies in the environmental field, and commonly used methods for in situ monitoring in the environment, including fluorescence in situ hybridization, real-time quantitative PCR, and amplicons sequencing technology.