In recent years, we have achieved low threading dislocation density in GaN wafers by using the Na-flux multi-point seed technique. However, the resulting wafers exhibit regions of high dislocation density, exceeding 105 cm−2 at the coalescence boundary where pyramidal crystals merge. In this study, we discovered that annealing seed crystals at 900 °C generated an uneven surface with approximately 50 μm of GaN decomposition, and growing GaN on the thus-generated uneven surfaces induced lateral growth composed of facets. We then investigated the effect of the uneven surface on dislocation reduction and found that the average threading dislocation density of the grown crystal was reduced from cm−2 in the seed crystal to cm−2. We confirmed that the reduction in threading dislocation density was due to the termination of dislocations by means of inclusions, and to mergers or annihilation as they encountered one another during facet growth.