What is less clear, though, is how well he will get along with the uniformed military.
Jones is a retired commandant of the US Marine Corps and is held in high regard as a senior commander and combat veteran. Donilon has never served in the armed forces.
There’s a risk that "the White House will have lost a credible voice with the US military in losing Jones," says Andrew Exum, a fellow with Center for a New American Security and a former US Army ranger.
In his recent book “Obama’s Wars,” Bob Woodward portrays Jones as resentful of some of the more political White House insiders. Reportedly he once upbraided then White House chief of staff Rahm Emanuel when Emanuel went around Jones to discuss an issue with his close friend Donilon.
Woodward also writes that Defense Secretary Robert Gates “felt that Donilon did not understand the military or treat its senior leadership with sufficient respect.”
“The secretary later told Jones that Donilon would be a ‘disaster’ as Obama's national security adviser,” Woodward writes.
During a press conference with the South Korean Minister of Defense Friday, Secretary Gates felt compelled to dispel that view.
"I have had a very productive and good working relationship with Tom Donilon, contrary to what you may have read, and I look forward to continuing to work with him,” said Gates, who is expected to leave the administration next year.
The Gates-Donilon flap apparently came over the administration’s review of US policy in Afghanistan – specifically, whether to increase US troop levels there and by how much. Jones and Donilon both questioned the need for additional troops, as did Biden. Donilon will now be overseeing a major review of the war in Afghanistan due out early next year.
Donilon's relationship with Republicans could also be an issue. During his time in Washington, Donilon also worked at mortgage giant Fannie Mae from 2000 to 2005. A government report accused him of leading a campaign against investigations into accounting irregularities at Fannie Mae.
Jones has long said he will leave the Obama administration by the end of this year. His resignation is just the latest in a series of departures by senior administration officials, some voluntary, some forced.
Those having left or soon to leave include:
- White House Chief of Staff Rahm Emanuel.
- Lawrence Summers, director of the National Economic Council.
- Council of Economic Advisers Chair Christina Romer.
- White House Social Secretary Desiree Rogers.
- Director of National Intelligence Dennis Blair.
- Director of the Office of Management and Budget Peter Orszag.
• Pentagon correspondent Anna Mulrine contributed to this report.