The north-central Patagonian coast is the sea lions most abundant area in Argentina. As occurs along the entire Atlantic coast, the distribution of breeding colonies at this smaller geographical scale is also patchy, showing at least three areas with breeding activity. We study the genetic structure and historical population dynamics of the species in five colonies in this area, analysing a 508 base-pair segment of the D-loop control region. Otaria flavescens showed 10 haplotypes with 12 polymorphic sites. The genealogical relationship between haplotypes revealed a shallow pattern of phylogeographic structure. The analysis of molecular variance showed significant differences between colonies, however, pairwise comparisons only indicate significant differences between a pair of colonies belonging to different breeding areas. The pattern of haplotype differentiation and the mismatch distribution analysis suggest a possible bottleneck that would have occurred 64,000 years ago, followed by a demographic expansion of the three southernmost colonies. Thus, the historical population dynamics of O. flavescens in north-central Patagonia appears to be closely related with the dynamics of the Late Pleistocene glaciations.