The Steiler sea lion (Eumetopias jubatus) is a threatened species that has experienced significant population declines over the past 3 decades. Previous genetic studies indicated low allozymic variability in this monotypic species. However, high levels of variation exist in the mitochondrial control-region, as revealed by a 238 base-pair sequence from 224 specimens taken over most of the range of the species. Patterns of macrogeographic variation indicate the presence of two genetically differentiated populations of Steiler sea lions. A western population included rookeries from the Commander Islands in Russia and the Aleutian Islands and Gulf of Alaska in Alaska. An eastern population included rookeries from southeastern Alaska and Oregon. Phenetic analysis of the mitochondrial-DNA (mtDNA) haplotypes indicates that certain haplotype lineages are specific to one or the other populations. Thus, these populations have been separated for a sufficient amount of time to allow diversification of lineages. However, the two populations are paraphyletic with respect to mtDNA, which indicates that they do not trace their ancestries back to a single maternal ancestor in either case. The populations likely diverged as a result of separation in different glacial refugia.