Vertically aligned Zinc Oxide rod arrays were grown by the self-assembly hydrothermal process on the GaN epitaxial layer which has a same lattice structure with ZnO. Zinc nitrate and DETA solutions are used in the hydrothermal process. The thin film was deposited on GaN and the patterning was made by the photolithography technique. The selective growth of ZnO rod was achieved with the patterned GaN substrate. The fabricated ZnO rods are single crystal, and have grown along hexagonal c-axis direction of (002) which is the same growth orientation of GaN epitaxial layer. The density and the size of ZnO rod can be controlled by the pattern. The optical property of ordered array of vertical ZnO rods will be discussed in the present work.