The South American sea lion, Otaria flavescens, has been considered vulnerable and under the threat of extinction in Peru due to the drastic demographic changes as a result of the impact of low food availability and the unusual timing of the severe El Niño event of 1997-1998. We present the first estimate of effective population size (Ne ) for the species that takes into account the effects of mating system and variation in population size in different generations caused by the severe El Niño event of 1997-1998. The resulting Ne was 7715 specimens. We believe that the estimated Ne for the Peruvian population is not a critical value, because it is higher than the mean minimum viable population generally accepted for vertebrates (ca. 5000 breeding adults). However, the viability of O. flavescens on the Peruvian coast may depend primarily on local availability of food resources. Climatic change models predict stronger and more frequent El Niño events. In this sense, the Ne of 7715 should be considered as a value to be maintained in order to keep the population large enough to avoid inbreeding or to retain adaptive genetic variation to survive to future El Niño events. Moreover, this Ne estimate is important data in discussions about resuming culling activities, based on the statement of an increasing competition between fishery activity and sea lions during El Niño events. Thus, this Ne should be taken into account in future management plans to ensure the conservation of the species on the Peruvian coast. © 2012 Marine Biological Association of the United Kingdom.