Genetic variation at 6 nuclear microsatellite loci with biparental inheritance and the maternally inherited mitochondrial DNA (mtDNA) was studied at 3 geographic scales (rookeries, regions, and stocks) in Steller sea lions (Eumetopias jubatus). Genetic variation was high in both nuclear and mtDNA markers as revealed by a near range-wide survey of 21 rookeries. However, population structure was not well defined, and there was no obvious phylogeographic pattern to the distribution of microsatellite alleles. This contrasts with a clear phylogeographic pattern revealed by control-region sequences of mtDNA in which 2 well-differentiated stocks, eastern and western, are defined as well as 2 distinct groups, Asian and central, in the western stock. Effective migration estimates are consistently higher for the nuclear loci than for mtDNA. The difference in patterns between the biparentally and maternally inherited genetic markers can be explained by relatively high male dispersal rates and female philopatry, or else there has been insufficient time since populations have been isolated for the nuclear loci to have diverged. It is recommended that the presently accepted stock structure be retained for management purposes and that further studies be carried out to test the male dispersal hypothesis.