The Japanese golden eagle (Aquila chrysaetos japonica) is an endangered subspecies inhabiting Japan and parts of Korea. Its population size has dropped to 500 individuals in the wild, due to habitat degradation and consequent reduced breeding success. It is crucial to conduct genetic studies of the Japanese golden eagle for understanding the state of inbreeding depression, and to monitor genetic diversity in wild and captive populations. Previously studied genetic markers (16 microsatellite loci, n=54) revealed relatively high genetic diversity (Ho=0.528) and low levels of inbreeding (F=0.087) compared to other endangered species, and there was no significant difference between wild and captive populations. Current markers are usable for individual identification (P-ID=8.6×10^-11), but not yet sufficient for kinship analyses. In order to improve the power of these analyses and to perform kinship analyses, we are developing new, hypervariable microsatellite markers. So far, we have found 27 polymorphic loci, and are currently testing their suitability to use with noninvasive samples. We will genotype samples from the wild (provided by collaborators in the field) and from captivity (given to us by zoos) at these loci to create genetic profiles for individuals, track their movements, and evaluate their genetic diversity.