Microbial communities play critical roles in global biogeochemistry cycling of many elements. However, the classical methods for studying such communities can only provide incomplete genetic structure data, but cannot effectively link microbial community structures to their functions. This mini review summarizes the recent developments and applications of some biomolecular methods. These include the use of mRNA and rRNA simultaneous fluorescence in situ hybridization, oligonucleotide microarrays, stable isotope enrichments, and other aspects of Metagenomics and Metaproteomics. Furthermore, future trends and perspectives are also discussed.