The crystallographic coalescence of crystalline silicon clusters into superlattice structures, generated by direct deposition of a silicon cluster beam on a graphene substrate, has been observed. High-resolution transmission electron microscopy and transmission electron diffraction analyses revealed that adjacent silicon clusters in the superlattices, having a mean diameter of 1.61 ± 0.05 nm (n = 109, n indicating the cluster size, Si n ) and an sp 3 diamond structure, form sp 3 covalent bonds between Si atoms on their surfaces and align their atomic crystalline axes, forming crystallographic rows to coalesce into bcc superlattice structures with a lattice constant of 2.134 ± 0.002 nm. The hcp configuration of the silicon clusters with the same lattice constant as the bcc superlattice unit cell is commensurate with the crystallographic structure of the graphene substrate. The absorption spectra confirm the sp 3 diamond structure of the silicon clusters under well-quantized conditions. Oxygen-free unoccupied electronic states (UDOS) in the conduction band of the silicon cluster superlattices appeared at 99.8 eV in the electron energy loss spectroscopy spectra. The s + d UDOS at 107.5 eV in SiO 2 became conspicuous as the oxidation of the specimen advanced. The collective bulk plasmon loss of the virtually oxygen-free silicon cluster superlattice appeared at 16.7 eV.