The H3N8 flu has been associated with the deaths of harbour seals in New England last year.
Researchers say the virus may have evolved from a type that had been circulating in birds.
They say the discovery highlights the potential for pandemic flu to emerge from unexpected sources.
Researchers were puzzled by the mysterious deaths from pneumonia of 162 harbour seals around the coast of New England last year.
Autopsies on five of the marine mammals indicate that they died from a type of H3N8 influenza A virus that is closely related to a strain circulating in North American birds since 2002.
One of authors of the research paper is Prof Ian Lipkin, from Columbia University in the US. He is a celebrated virus hunter who in the past has helped identify West Nile virus and Severe Acute Respiratory Syndrome (SARS). He told the BBC that finding this flu virus in seals was an interesting "new jump".
"It's something that's been circulating for a while in birds, but we've not had this sort of die off relating to this virus in the past. As we've looked at it in some detail, we've found there have been mutations in this virus which enable it to bind to both bird receptors for flu as well as mammalian receptors for flu."
Cause for concern
As well as mutating to live in both mammals and birds the scientists say this flu has evolved to make it more likely to cause severe symptoms. The virus also has the ability to target a protein found in the human respiratory tract.
Dr Anne Moscona of Weill Cornell Medical College in New York City edited the report and says that the new virus is a worry.