Herein, the annealing behaviors of defects in ion‐implanted GaN are studied by positron annihilation, cathodoluminescence, scanning transmission electron microscopy, and atom probe tomography. Si or Mg ions are implanted into GaN to obtain 300 nm deep box profiles of the impurities. The samples are annealed up to 1480 °C under a N2 pressure of 1 GPa. For as‐implanted GaN, the major defect species is identified as Ga‐vacancy‐type defects. After annealing above 1000 °C, vacancy clusters are introduced, and they remain even after 1480 °C annealing. For Mg‐implanted GaN with the Mg concentration ([Mg]) ≤ 1018 cm−3, no large change in the depth distribution of Mg is observed before and after annealing at 1400 °C. For the sample with [Mg] = 1019 cm−3, however, Mg diffuses into the bulk, which is attributed to the over‐doping of Mg and their vacancy‐assisted diffusion. The Mg diffusion is suppressed, and the donor–acceptor pair emission is enhanced by sequential N‐implantation, which is attributed to the reaction between Mg and vacancies under a N‐rich condition. For the samples annealed at 1480 °C, an accumulation of Mg around dislocation loops and Mg clustering are enhanced by the N‐implantation