One of the challenges the microbial ecologists are facing is the identification of microorganisms that are responsible for particular biochemical processes in the environment. Although small- subunit rRNA gene sequencing is a robust technique whereby the phylogenetic diversity of microbial communities can be described, it provides few direct links between the identity of microorganisms and their metabolic capabilities and function in the environment. In contrast, when a microorganism is cultivable, it can be identified, after isolation, and characterized at the physiological, biochemical and genetic level. However, only a small fraction of microorganisms present in the environment have been successfully cultivated. Stable isotope probing (SIP) techniques are based on analyzing biomarkers (nucleic acids or phospholipid-derived fatty acids) after microbial consumption of 13C- or 15N-labelled substrate added to an environmental sample. The use of SIP allows the direct detection of microorganisms that are truly active in the degradation and assimilation of a particular substrate within a complex microbial community. The main advantages of this method are its cultivation independence and the fact that it links the identity of microorganisms with their function in the environment.