Direct methane conversion into aromatic hydrocarbons over catalysts with molybdenum (Mo) nanostructures supported on shape-selective zeolites is a promising technology for natural gas liquefaction. We determined the identity and anchoring sites of the initial Mo structures in such catalysts as isolated oxide species with a single Mo atom on aluminum sites in the zeolite framework and on silicon sites on the zeolite external surface. During the reaction, the initial isolated Mo oxide species agglomerate and convert into carbided Mo nanoparticles. This process is reversible, and the initial isolated Mo oxide species can be restored by a treatment with gas-phase oxygen. Furthermore, the distribution of the Mo nanostructures can be controlled and catalytic performance can be fully restored, even enhanced, by adjusting the oxygen treatment.