This paper presents, for the first time, noninvasive imaging of a livingplant using biocompatible carbon-encapsulated AuAg nanoparticles (NPs) using micro-Raman spectroscopy (MRS). A convenient and controllable hydrothermal synthetic route was developed to synthesize the layer-by-layer triplex AuAgC core–shell NPs, which can incorporate the reporter molecule 4-mercapto benzoic acid (4-MBA). A unique approach was devised to deliver the carbon-encapsulated surface-enhanced Raman scattering (SERS) tags into the leaf of Nicotiana benthamiana. In vivo SERS mapping was subsequently performed to monitor the distribution of tags inside the leaf, which successfully avoided interference of autofluorescence from plant tissue. The imaging modality reported here and further the bio-functionalized carbon-encapsulated SERS NPshold significant potential as a strategy forbiochemical imaging in living plantsin a noninvasive and nontoxic manner, whichmight open up exciting opportunities for plant sciences. Copyright © 2010 John Wiley & Sons, Ltd.