Direct evidence of the successful incorporation of atomically dispersed molybdenum (Mo) atoms into the framework of nanosized MFI zeolite is demonstrated for the first time. Homogeneous distribution of Mo with a size of 0.05 nm is observed by scanning transmission electron microscopy high-angle annular dark field imaging (STEM-HAADF). P-31 magic-angle spinning nuclear magnetic resonance (MAS NMR) and Fourier transform infrared (FT-IR) spectroscopy, using trimethyl-phosphine oxide (TMPO) and deuterated acetonitrile as probe molecules, reveal a homogeneous distribution of Mo in the framework of MFI nanozeolite, and the presence of Lewis acidity. P-31 MAS NMR using TMPO shows probe molecules interacting with isolated Mo atoms in the framework, and physisorbed probe molecules in the zeolite channels. Moreover, 2D P-31-P-31 MAS radio frequency-driven recoupling NMR indicates the presence of one type of Mo species in different crystallographic positions in the MFI framework. The substitution of framework Si by Mo significantly reduces the silanol defect content, making the resulting zeolite highly hydrophobic. In addition, the insertion of Mo into the MFI structure induces a symmetry lowering, from orthorhombic (Pnma), typical of high silica MFI, to monoclinic (P21/n), as well as an expansion of unit cell volume. The novel material opens many opportunities of catalysts design for application in mature and emerging fields.