The South American sea lion (Otaria flavescens) is a pinniped known to interact with fisheries, potentially damaging gear and lowering catches. Predation by O.flavescens and spiny dog fish (Squalus acanthias) on artisanal southern hake (Merluccius australis) catches in fjords of Chilean Patagonia is estimated and compared. Observations were made in the Gulf of Ancud and Comau Fjord in southern Chile from October 2005 to September 2006. Losses of southern hake catches to O. flavescens predation were 1.6% of the total catch of the species, and to spiny dog fish predation were slightly higher, at 3.3%. The predation of both species on southern hake catches varied throughout the year, but was lower in summer. Both predators showed a preference for adult southern hake over juveniles. There was no significant relationship between predation on southern hake catches by the sea lion and the availability of adult and juvenile southern hake on longlines (AHCL). However, there was a significant relationship (p < 0.05) between AHCL and spiny dog fish predation. Most O.flavescens interaction events (81.4%) were during longline retrieval. Our results showed minimal interactions between O.flavescens and the artisanal southern hake fishery in the area, so with the present abundance of O.flavescens, there is no justification for reducing the sea lion population by hunting.