(CNN) - President Obama anounced Friday that retired Marine Gen. Jim Jones is stepping down as White House National Security Adviser and will be replaced by his current deputy, Tom Donilon.
The move has been long anticipated because senior officials say Jones never quite clicked with other key members of Obama's inner circle. Jones was not an active part of the Obama presidential campaign and two people close to Jones tell CNN that when he accepted the appointment in 2009 he only agreed to stay on for two years.
The turnover comes after a slew of other top Obama aides have left the White House or signaled their plans to leave the administration either later this year or in early 2011, including Chief of Staff Rahm Emanuel, senior adviser David Axelrod, and top economic aides Larry Summers and Christina Romer.
But the choice of Donilon, a well-known quantity inside the West Wing, signals that even during a time of turnover Obama is someone who prefers to replenish the ranks with people from his inner circle. Given that approach, top Democratic advisers privately say it is highly unlikely that Obama will go far outside the circle when he eventually settles on a permanent chief of staff, despite expected pressure on the President to widen the circle after the midterm elections.
Continuity has reigned so far in the musical chairs of staff moves. Romer was replaced as chair of the White House Council of Economic Advisers by White House economic aide Austan Goolsbee, while Axelrod is expected to be replaced next year by someone already in the fold like Press Secretary Robert Gibbs or former Obama campaign manager David Plouffe while Axelrod moves to Chicago but stays on as an informal adviser on the expected 2012 re-election effort.
Earlier this month, Emanuel was replaced as chief of staff on a temporary basis by longtime Obama aide Pete Rouse. Donilon had been rumored to be a possible permanent successor to Emanuel, but two sources familiar with the conversation told CNN that Donilon recently told the President he wanted to take himself out of the running for chief of staff and instead stay at the National Security Council, knowing full well that Jones was likely to leave soon and he was expected to move up.
Jones' exit brings to a close a somewhat-tumultuous time as National Security Adviser, after he clashed with Emanuel and other top White House officials, in part because of a hands-off style that did not sit well with administration officials who were expecting a more take-charge leader at a time of wars in Afghanistan and Iraq, as well as a slew of thorny national security challenges.
In his defense, Jones allies note he is a highly-respected former Marine Commandant and NATO's Supreme Allied Commander in Europe. These allies note that Obama, a commander in chief who came to the job without military experience, benefited from the credibility within the military that Jones brought to the table.
Jones will now be replaced by Donilon, who is widely hailed in Democratic circles as a sharp foreign policy mind, including his tenure as chief of staff to then-Secretary of State Warren Christopher in the Clinton administration.
But Donilon has himself clashed with some in the Obama orbit as well. Journalist Bob Woodward, in his new book "Obama's Wars," suggests there has been tension between Donilon and Defense Secretary Robert Gates.
"Gates felt that Donilon did not understand the military or treat its senior leadership with sufficient respect," Woodward wrote. "The secretary later told Jones that Donilon would be a 'disaster' as Obama's national security adviser."
But a senior Defense official told CNN that "the Woodward characterization is just way out of date" because Gates and Donilon now have a "strong working relationship" within the administration.
Nevertheless, the Defense official acknowledged "they had some issues" during the sometimes-contentious internal "Af-Pak" debate last fall that resulted in the President crafting a new policy toward Afghanistan and Pakistan, which resulted in Obama announcing a surge of 30,000 more U.S. troops being sent to Afghanistan.
"They have long since been overcome," the senior Defense official said of the tensions.
Gates himself told reporters on Friday, "I have thoroughly enjoyed working with General Jones and I have and have had a very productive and very good working relationship with Tom Donilon, contrary to what you may have read. And I look forward to continuing to work with him."
Donilon's appointment, however, may ruffle some other feathers within the administration. Several of Obama's foreign policy advisers during the campaign, who were angling for the National Security Advisor job after the election but did not get the nod in 2008, were also considered contenders to replace Jones this time and might have been considered more inspired choices than Donilon.
U.S. Ambassador to the United Nations Susan Rice, a former Assistant Secretary for African Affairs and scholar at the Brookings Institution, was one of Obama's most public foreign policy voices during the campaign. She is said to be disappointed with the New York job because she was lobbying hard to be National Security Adviser after Obama's election victory and aides have said she would have wanted to move back to Washington to take the post if Jones left.
Deputy Secretary of State James Steinberg, who was Deputy National Security Adviser in the Clinton administration, also wanted the job before it was given to Jones. Instead he was sent to the State Department and there has been speculation he wants out, hoping to land a top staff job at the White House.
–CNN Senior State Department Producer Elise Labott contributed to this report.