The Sea Otter is considered to be Endangered due its vulnerability to large-scale population declines. The species is believed to have undergone a decline exceeding 50% over the past 30 years (approximately three generations). The world-wide population of Sea Otters decreased to approximately 2,000 animals by the end of the commercial fur trade in 1911 (Kenyon 1969). The population recovered from 11 remnant populations located in Russia (Bering Island, Kamchatka Peninsula, and Kuril Islands) and in the United States (in Alaska (Aleutian Islands, Alaska Peninsula, Kodiak archipelago, and Prince William Sound) and California). The remnant populations were small and widely dispersed, as a result, this species has low genetic diversity (Ralls et al. 1983). Since the 1980s, the species had been recovering in many areas thanks to intensive management and regulatory efforts by several governments. However contemporary issues (oil spills, potential fisheries interactions, predation, and disease events), have either prevented Sea Otter populations from thriving or have caused population declines throughout much of the species range. In the United States, two subspecies of Sea Otters are listed as threatened (E. lutris kenyoni in SW Alaska and E. lutris nereis in California) due to precipitous population declines in Alaska and slow growth (and vulnerability to anthropogenic factors) of a small population in California.

In Alaska, precipitous population declines occurred in the Aleutian Islands beginning in the late 1980s–2005. By 2000, counts of Sea Otters had decreased by 90% with a declining trend through 2005 (Doroff et al. 2003, Estes et al. 2005, Burn et al. 2003). The probable cause of the decline was increased predation by killer whales (Orcinus orca) (Estes et al. 1998). More recent Sea Otters surveys indicate the population trend has increased since 2005, however, counts remain well below carrying capacity for this region (D.M. Burn pers. comm. 2010). Population counts also remain low for the Alaska Peninsula (Burn and Doroff 2005, U.S. Fish and Wildlife Service Stock Assessment Reports). The population in the Kodiak archipelago and lower Cook Inlet appeared stable or increasing during the same period that population declines were documented in the Aleutian Islands and Alaska Peninsula (Kodiak and lower Cook Inlet are part of the Southwest population stock), however, this habitat has not been surveyed since 2004.

Recent studies have found infectious disease to be an important mortality factor in California Sea Otter populations (Conrad et al. 2005, Johnson et al. 2009). Information collected from forensic-level necropsies of dead Sea Otters and sampling of free-ranging Sea Otters indicate a strong link to protozoan parasites, Toxoplasma gondii and Sacrocystis neurona, that are known to breed in cats and opossums (Thomas and Cole 1996, Conrad et al. 2005) thus sources of mortality for the Sea Otter population include land-based factors. Other factors identified as causing significant mortality include acanthocephalan peritonitis, protozoal encephalitis, bacterial and fungal infections (Thomas and Cole 1996).

The situation in the Russian Federation is clearer now. The Sea Otter number on the Commander Islands reached maximum since last 150 years period (A. Burdin and S.V. Zagrebelny pers. comm. 2006). In 2007, the direct count revealed around 8,000 otters in both Bering and Medny Islands. The Commanders Island population of Sea Otter was never so abundant, but in 2008, it was found that the population was on decline. In 2004 the Kuril Islands population of Sea Otter was estimated around 19,000 (Kornev and Korneva 2004), but later count have shown sever decline (up to 40–50% in different locations). Though the causes of such decline are not very clear, the threat due to poaching can’t be ruled out.