islands are induced by molecular beam epitaxy of sub-monolayer transition metal Cr on top of GaN pseudo "1 × 1" surface. By scanning tunneling microscopy (STM) study at the atomic scale, we found that the 2D islands were constructed by periodic superstructures. They were detected to be bright spots using a typical W tip, whereas using Fe-coated W (Fe/W) tip scanning, they exhibit as superstructures of Cr−Ga complex lattices with the ratio of Cr:Ga = 3:1. Vacancy defects were observed in the superstructures, and they are active during STM imaging, forming multiple movable behaviors, such as creation, annihilation, and neighboring exchange. The discovery of the new Cr−Ga superstructures and their active defects would potentially inspire research on exploring unique properties in the Cr−Ga system and its related atomic defect engineering.