Hybridization has a large impact on the generation and maintenance of biodiversity. However, genetic integrity among distinct lineages and populations has the potential to be eroded through admixture, thus directly influencing evolutionary trajectories and management policies. Mule deer (Odocoileus hemionus) are an important and intensively managed game species in California. We examined the genomic evidence for six putative mule deer subspecies resident to California using low coverage (~1.1X) whole genome resequencing data. We also used whole mitogenomes to evaluate the evolutionary relationships between mule deer in California and white-tailed deer (Odocoileus virginanus). Principal component and admixture analyses based on ~215,644 SNPs recovered varying levels of differentiation among putative subspecies. Our results primarily supported the presence of Columbia black-tailed, Rocky Mountain, Southern, and California mule deer lineages with pronounced admixture in regions of sympatry. Our mitogenome phylogenetic estimate suggested close affiliation of Rocky Mountain mule deer in northeastern California with white-tailed deer, similar to previous studies of those two lineages in other regions of North America. Our findings offer insights into the geographic scale of genetic structure and admixture among mule deer subspecies in California, which provides a foundation for future research on adaptative introgression and aid in management decisions.