The microstructural properties of a GaN layer grown on a patterned sapphire substrate (PSS) were studied in detail using transmission electron microscope techniques to determine dislocation and growth behaviors. Regular and uniform recrystallized GaN islands were observed on the protruding pattern. On a flat sapphire surface, the crystallographic orientation relationship of ⟨1¯21¯0⟩GaN on FS//⟨11¯00⟩sapphire and {11¯01}GaN on FS//{12¯13}sapphire existed between the GaN and the substrate. On the other hand, the orientation relationship of ⟨1¯21¯0⟩GaN layer//⟨1¯21¯0⟩GaN island on IS//⟨11¯00⟩sapphire and {11¯01}GaN layer//{0002}GaN island on IS//{12¯13}sapphire was confirmed among the GaN layer, the recrystallized GaN islands on an inclined sapphire surface and the PSS. The flat surface among the protruding patterns began to fill rapidly with GaN. Then, the GaN gradually overgrew the protruding pattern and coalesced near the summit as the growth time increased. The generation of threading dislocations was observed in the vicinity of the coalescence points near the top of the protruding patterns.