We investigate the phylogeography of California (Zalophus californianus) and Galápagos (Z. wollebaeki) sea lions and describe within-population structure for the California sea lion based on mitochondrial DNA. Fifty control-region haplotypes were found, 41 from Z. californianus and 9 from Z. wollebaeki, with three fixed differences between the two species. Ranked population boundaries along the range of Z. californianus were defined based on the Monmonier Maximum Difference Algorithm, resulting in five genetically distinct populations, two in the Pacific Ocean and three inside the Gulf of California. A Minimum Spanning Network showed a strong phylogeographic signal with two well-defined clusters, Z. californianus and Z. wollebaeki, separated by six base-pair differences, supporting the existence of two genetically distinct species with an estimated divergence time of ˜0.8 Ma. Results are discussed in the context of the historical geologic and paleoceanographic events of the last 1 Ma in the eastern Pacific.