This paper reports the synthesis and characterization of self-assembled ZnO nano-dots deposited on SiN x /Si(001) substrates by radio frequency magnetron sputtering. The effect of the working pressure on the microstructure of the as-grown ZnO thin films was examined. At a working pressure of 6 × 10 − 3 Torr, a flat layered structure was dominant with a preferred orientation of the ZnO(0002) plane, while ZnO nano-structures were observed on the samples grown at 2 × 10 − 2 Torr. This was attributed to the columnar growth that facilitated the nucleation of ZnO nano-structures on the growing surfaces. Hexagonal nano-pyramids were formed, which then transformed into nano-dots as the film became thicker. The ZnO nano-dots were uniform and well dispersed, exhibiting distinct photoluminescence spectra due to the quantum confinement effect.