The northern coast of the San Jorge Gulf, Atlantic Patagonia, is recognised as a marine biodiversity hot spot and is designated as a priority conservation area. Among marine mammals, three species of pinnipeds inhabit the region. While South American sea lions ( Otaria flavescens) have a higher abundance and a larger number of colonies than South American fur seals ( Arctocephalus australis), a few individuals of the Southern elephant seal ( Mirounga leonina) reside in the region. Nevertheless, little is known about the abundance and distribution of these pinnipeds before the 18th century, when various extractive activities became widespread, including the unregulated exploitation of furs and oil. This study aims to examine whether the distribution and relative abundance of ancient pinnipeds differ from present-day populations. To achieve this, we conducted inter-specific identification of pinniped bone remains coming from archaeological assemblages dated from 6000 to 600 14C years BP and reviewed historical sources to contrast these retrospective data with modern ecological literature. The results suggest changes over time in the relative abundances of species within the pinniped community. The relative abundance of fur seals was greater than or equal to that of sea lions in most Late-Holocene pinniped assemblages. Additionally, fur seals have been recorded in historical and Late-Holocene periods in places where they are currently very rare. These findings are consistent with the higher relative abundance of fur seals recorded in other archaeological sites along the Patagonian coast, suggesting that modern distribution and abundance have been heavily affected by commercial hunting. This study contributes to a better understanding of the nature and magnitude of the anthropic impact on the marine ecosystem of the northern coast of the San Jorge Gulf. It also provides historical baseline information to strengthen conservation policies and restoration efforts.