Stable isotope probing (SIP) is a series of techniques by combining stable isotope labeling with molecular methods. SIP links microbial function and interactions with identity without isolated culture, which avoids the drawback of pure culture and extends the available boundary of microbial resources. The application of SIP to identify functional microorganisms in organic pollutant biodegradation has a bright prospect. This review introduces the fundamental principal and procedure of SIP, the characteristic of PLFA-SIP, DNA-SIP and RNA-SIP, and the application of SIP in biodegrading organic pollutants (Benzene, Toluene, Ethylbenzene and Xylene (BTEX); Polycyclic aromatic hydrocarbons (PAHs); Polychlorinated biphenyls (PCBs)). Future prospect of SIP in rhizospheric biodegradation is also presented.