Similar to all of the other southern fur seals, Subantarctic Fur Seals were over-exploited by sealers in the 18th and 19th century and were reduced to the brink of extinction at the beginning of the 20th century. Since then their population has increased rapidly and they have reoccupied much of their former range. This population bottleneck has reduced their genetic variation and may render this species vulnerable to disease or climate change (Wynen et al. 2000).

Tourist visits at Subantarctic Fur Seal haulout sites are rare and thought to cause minimal disturbance (Kirkwood et al. 2003, Shirihai 2002). Few fisheries take place in waters occupied by this species (Hanchet et al. 2003). Entanglement in marine debris occurs at the Prince Edward Islands, but with incidences of less than 1% (Hofmeyr et al. 2002).

While the impact of climate change on fur seals is unknown, it is potentially detrimental (Chown et al. 1998, Learmonth et al. 2006). Fur seals are also at risk of mass mortality from infectious diseases, though breeding on isolated islands affords some species a higher degree of protection from disease (Chown et al. 1998, Lavigne and Schmitz 1990).