In this study, we report the application of synchrotron radiation microprobe to the analysis of Mn-rich clusters in GaN. From the Mn and Ga fluorescence line intensity ratio, an average Mn concentration of 11% was deduced. A combination of fluorescence mapping with spectroscopic techniques enabled us to examine not only the cluster elemental nature but also their crystallographic orientation on the submicron scale. The strong polarization-dependent x-ray absorption near-edge structure features showed the preservation of the hexagonal symmetry in both cluster-free and Mn-rich regions. However, from the x-ray absorption data taken inside the clusters, a preferential disorder was observed in the direction parallel to the crystal growth rather than perpendicular to it. © 2005 American Institute of Physics.