Stomach contents of South American (Arctocephalus australis) (n = 219) (SAFS) and sub‐Antarctic (A. tropicalis) (n = 37) (SFS) fur seals were opportunistically sampled from 1980 to 2021 to examine their feeding habits and resource partitioning in southern Brazil while in their nonreproductive periods. SAFSs mainly consumed abundant coastal pelagic species, such as Anchoa marinii and Doryteuthis sanpaulensis, resulting in high sexual trophic niche overlap. The frequency of occurrence (%FO) of fish prey, especially the overexploited Micropogonias furnieri, decreased between 1980–1992 and 2007–2021, while squid increased. For SFSs, offshore squids such as Ommastrephes bartramii and Illex argentinus were the most important prey considering both sexes in the long‐term. The interspecific trophic niche overlap was low, but it is likely underestimated since it increased with the inclusion of scat samples from SFSs. This sample‐size effect was also observed in Shannon's diversity index, which was lower for underrepresented SFSs. Marine debris ingestion was detected in both species (SAFS %FO = 2.7; SFS %FO = 8.3), with only flexible plastic material found. This study brings novel information on feeding habits of fur seal species in the extreme south of Brazil, as well as unprecedented information about their ecology during the nonreproductive period.