This chapter summarizes the applications of stable isotope probing (SIP) technology in plant-soil systems and presents an overview of the progress achieved in the understanding of the plant-soil microbe interactions and their role in ecosystem functioning. The applications of phospholipid fatty acids-based SIP (PLFA-SIP) and then the applications of DNA- and RNA-based SIP in upland soils and flooded rice field soils, respectively, are described. Several studies have exploited PLFA-SIP technology to determine the plant-microbe interactions driven by rhizosphere carbon flow. In these studies, the living plants, either in the field or laboratory, are exposed to 13C-labeled CO2, and the microbial PLFAs are collected from rhizosphere soil. After pulse-labeling of rice plants with 13CO2 in a microcosm, soil samples were divided into rhizosphere and bulk soil, and the bulk soil samples were further partitioned vertically into upper layer and lower layer and horizontally into five layers with an increasing distance from roots. A study performed on grassland soil and on peatland soil, targeted mainly the root symbiont's arbuscular mycorrhizal (AM) fungi and the bacteria possibly associated with them. RNA-SIP revealed that AM fungi were labeled with 13C immediately after plant assimilation, suggesting that AM fungi preferentially used assimilates provided by plants rather than previously fixed carbon. Combining SIP with techniques such as metatranscriptomics, pyrosequencing, and community systems biology, promises a better and deeper understanding of plant-microbe interactions.