The golden eagle is an apex predator found across the northern hemisphere, with a diverse range expanding throughout California. Despite its ubiquity, little is known regarding genetic diversity, population structure, and environmental influences on genetic variation. Here, we present a whole-genome resequencing dataset of 146 North American golden eagles (Aquila chrysaetos canadensis) alongside a new reference assembly to evaluate patterns of genetic variation across California and adjacent states. Our assembly improves upon previous versions, rivaling other high-quality Accipitridae reference genomes. We identified ~5 million SNPs after quality filtering, resulting in the most robust genomic dataset for this subspecies to date. Principle components analysis revealed population structure east and west of the Sierra Nevada Range suggesting its importance as a partial barrier to gene flow or potential philopatry to ecoregion. Further, genotypes from the south coast were broadly distributed throughout PC space, consistent with frequent immigration from other populations and suggesting this region may represent an ecological sink. Future analyses will assess patterns of inbreeding and environmental influences on genomic variation. With growing concern for golden eagle viability in California, understanding how genomic variation is geographically partitioned will aid management efforts.