Intraspecific patterns of mitochondrial DNA sequence variation were determined among California sea lions (Zalophus califomianus californianus) from three colonies along the Pacific coast of southern and Baja California and one colony in the Gulf of California. We found no variation in 368 base pairs (bp) of cytochrome b sequence among 40 sea lions from these localities, but analysis of 360 base pairs of control region revealed eleven genotypes. The four genotypes found in the Gulf of California population were unique and phylogenetically distinct from those found in sea lions along the Pacific coast. The average sequence divergence between Gulf and Southern California genotypes was 4.3%, suggesting a relatively long period of isolation. However, colonies along the Pacific coast, which are less than 200 km apart, shared mtDNA genotypes, indicating that recent genetic exchange has occurred between them. Therefore, we suggest that regional female philopatry exists in California sea lions. Regional boundaries may be related to oceanic currents or patchiness in the distribution of resources. Further research is needed to better understand the underlying causes of genetic differentiation in the California sea lion.