We found that GaN:Gd known as one of the diluted magnetic semiconductors has two types of the thin-layer single crystal (Type-1 and Type-2) under different growth conditions. These crystals show different XRD profiles and X-ray absorption near edge structure at the Gd L3-edge. We measure Gd L3-edge XANES spectra and apply multiple scattering calculations to obtain the information of the local stereo structure around the Gd ion in GaN:Gd. In the Type-1 crystal, the calculations suggest that dopant Gd ions are substitued with Ga ions, and the Gd-N bond length is longer than the Ga-N length in GaN crystal. On the other hand, Type-2 crystal has at least one nitrogen vacancy adjacent to the substituted Gd ion, and furthermore the nitrogen vacancy is not in the c-axis around the Gd ion.