Elucidating the genetic structure and ascertaining the natal origin of Golden Eagles (Aquila chrysaetos) are challenging for a number of reasons, including the lack of highly reproducible, variant genetic loci. Here, we developed a new high-quality Golden Eagle genome reference to serve as a computational atlas for future genetic investigations. We then generated unique genetic resources for the Golden Eagle by performing low-coverage genomic sequencing for 32 individuals ranging from Alaska to southern New Mexico and California to Nebraska. By aligning the reads from these 32 individuals to our Golden Eagle reference genome, we detected approximately 900,000 population variants in the form of Single Nucleotide Polymorphisms (SNPs). Using linkage disequilibrium and other quality filters, we next derived a set of 30,006 SNPs that were used to cluster our samples into three genetic groups. Although additional work is needed to fully characterize these loci, we provide a high-quality Golden Eagle genome reference and a comprehensive set of genetic markers for the conservation and management of Golden Eagles. Additionally, with a more comprehensive Golden Eagle genome assembly and associated transcriptomes, it is now possible to target specific genes or other biologically relevant regions for evaluating the effects of many anthropogenic stressors on Golden Eagle survival.