A total of 676 elk (Cervus elaphus) were genotyped at 16 tetranucleotide microsatellite loci to evaluate genetic differences among 3 subspecies of elk in California: tule (C. e. nannodes), Roosevelt (C. e. roosevelti), and Rocky Mountain (C. e. nelsoni) elk. Of the 13 populations analyzed, 5 represented tule elk herds, 3 were Roosevelt elk, 2 were Rocky Mountain elk, and 3 were of uncertain taxonomic status. Overall, populations averaged between 7 and 8 alleles per locus, with observed heterozygosity values ranging from 0.33 to 0.58 per population. Tule elk, which experienced a severe bottleneck in the 1870s, had consistently less genetic diversity than the other subspecies. All 3 subspecies were significantly differentiated, with the greatest genetic distance seen between the tule and Roosevelt subspecies. Assignment of individuals to subspecies using microsatellite data was nearly 100% accurate. Despite the past population bottleneck, significant differences were found among the tule elk herds. Assignment testing of elk from Modoc, Siskiyou, and Shasta counties to determine subspecific status of individuals suggested that these populations contained both Roosevelt and Rocky Mountain elk and their hybrids, indicating that these elk subspecies interbreed where subspecies coexist.