Stable isotope probing (SIP), a combination of isotope labeling with molecular biological approach, is a technique that is used to identify microorganisms in environmental samples, and at the same time, to examine microbial functions during the biogeochemical processes operating in various environmental systems. The method has the potential for wide applications in the future, since it c an provide abundant information about microbial interactions and metabolic functions in complex communities. The rationale of the SIP technique is as follows. Environmental samples in situ or in microcosm are exposed to substrates labeled with stable isotopes. Some microorganisms in these samples can metabolize the stable isotope-enriched substrates as their carbon or nitrogen resource for growth. The stable isotope assimilated by these microorganisms is then used to synthesize cellular components such as nucleic acids (DNA and RNA) and phospholipid fatty acids (PLFA). As a result, the microbial identity can be linked to their functions by extracting and analyzing these stable isotope-labeled biomarkers in the microbial communities. Here, with introduction to the range of stable isotope enriched substrates, the labeling techniques of such substrates to microorganisms, and the selection criteria of appropriate biomarkers and the methods for extracting and analyzing the biomarkers, we illustrate the applications of SIP in the functional analyses of methylotrophs, bacteria of organic pollutants degradation, rhizosphere-microorganism ecology, syntrophic microorganisms and metagenomics.