Sequence variation in the mitochondrial DNA (mtDNA) control region was analyzed from 1,568 individuals representing nearly every rookery (n = 50) at which Steller sea lions (Eumetopias jubatus) are known to breed in significant numbers. Rookeries were grouped into regions and regions into stocks to examine structure at different spatial scales. Haplotype diversity (H = 0.9164 ± 0.0035) was high and nucleotide diversity (π = 0.00967 ± 0.00586) was moderate. No evidence was observed for significant genetic bottleneck effects. Previous studies of mtDNA recognized 2 stocks (eastern and western) and suggested the presence of 2 groups within the western stock. In this study, significant (P < 0.05) divergence of eastern stock (southeastern Alaska to California) animals from western stock animals was supported in analyses at all spatial scales. Likewise, rookeries and regions from Asia were found to be significantly different from all other western stock rookeries. This was most clearly demonstrated in regional comparisons. The Commander Islands rookery clearly associates with Alaskan western stock rookeries, not with the Asian rookeries. Within each of the 3 stocks there is significant isolation by distance among rookeries. This relationship does not hold for interstock comparisons, indicating that there are important barriers to gene flow among stocks. We recommend that the western stock be partitioned west of the Commander Islands, yielding a western stock that ranges from Prince William Sound west to the Commander Islands, and an Asian stock including rookeries from the Kamchatka Peninsula, Kuril Islands, and Sea of Okhotsk. The eastern stock remains unchanged and includes rookeries from southeastern Alaska through California.