Scientists at the University of California, Davis, detected the virus in free-ranging northern elephant seals.
"We thought we might find influenza viruses, which have been found before in marine mammals, but we did not expect to find pandemic H1N1," said lead author Tracey Goldstein, an associate professor with the UC Davis One Health Institute.
"This shows influenza viruses can move among species," said Goldstein.
Between 2009 and 2011, the team of scientists tested nasal swabs from more than 900 marine mammals from 10 different species off the Pacific Coast from Alaska to California.
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Neither infected seal appeared to be ill, indicating marine mammals may be infected without showing clinical signs of illness.
H1N1 originated in pigs. It emerged in humans in 2009, spreading worldwide as a pandemic. The World Health Organisation now considers the H1N1 strain from 2009 to be under control, taking on the behaviour of a seasonal virus.
"H1N1 was circulating in humans in 2009. The seals on land in early 2010 tested negative before they went to sea, but when they returned from sea in spring 2010, they tested positive. So the question is where did it come from?" said Goldstein.
The seals had been satellite tagged and tracked, so the researchers knew exactly where they had been and when they arrived on the coast.
The first seal travelled from California on February 11 to southeast Alaska to forage off the continental shelf, returning to Point Piedras Blancas near San Simeon, California, on April 24.
The second seal left Ano Nuevo State Reserve in San Mateo County, California, on February 8, travelling to the northeast Pacific and returning on May 5.
The study was published in the journal PLOS ONE.