A new synthetic route to functionalized single walled carbon nanotubes (SWNTs) via supramolecular interactions using a specifically designed naphthalenediimide (NDI) nanoreceptor is demonstrated. The tendency of the NDI to spontaneously form composites with carbon nanomaterials leads to fluorescent amino acid tagged SWNTs, which are dispersible in widely accessible organic solvents (CHCl3, DMSO) as well as in biocompatible cell medium (EMEM, Eagle's modified essential medium). The X-ray crystal structure of the first iodine-tagged and amino acid-functionalized NDI molecule, designed especially to facilitate the high resolution transmission electron microscopy (HR TEM) imaging whilst retaining its ability to self-assemble into a nanodimensional receptor in weakly polar solvents, is also described. A new hybrid material, NDI@SWNT, was prepared and characterized as dispersed in organic solvents and aqueous media and in the solid state by HR TEM, tapping mode atomic force microscopy (TM AFM), scanning electron microscopy (SEM), circular dichroism, Raman and fluorescence spectroscopies (steady-state single and two-photon techniques). Combined microscopy techniques, density functional theory (DFT) calculations using the Spanish Initiative for Electronic Simulations with Thousands of Atoms (SIESTA) program and spectroscopic measurements in solution indicate that amino acid-functionalized NDI interacts strongly with SWNTs and forms a donor-acceptor complex. Density functional theory (DFT) calculations predicted the geometry and the binding energies of an NDI molecule loaded onto a SWNT strand and the possibility of charge transfer interactions within the hybrid. The NDI@SWNT composite translocates into cells (e.g. FEK-4, HeLa, MCF-7) as an intact object and localizes in the cells' cytoplasm and partially in the nucleus. The NDI coating enhances the biocompatibility of SWNTs and mediates its intracellular localization as shown by confocal fluorescence imaging and fluorescence lifetime imaging (FLIM) techniques. The excited state fluorescence lifetime of the probes in cells versus solution phase indicates that the probes remain unaffected by the change in their chemical environment within the experimental timescale (2 h).