California-based Sergeant Gary Stein, a 26-year-old Iraq war veteran, was advised of the decision after a commanding general upheld the recommendation by a review board, Major Michael Armistead said.
"He was formally informed of that today, of the separating authority's decision. Now he will go through the transition required to leave the Marines," Armistead said, a process that can take up to 20 days.
Armistead said Stein was not considered a security risk during that time. Any discharge from the military that is not honorable can mean the loss of benefits available to most U.S. military veterans.
The Marines have said they initiated disciplinary proceedings against Stein, a meteorologist at Camp Pendleton, after he posted political statements about Obama - who is commander in chief of the U.S. military - on a Facebook page he ran called the "Armed Forces Tea Party."
In an account he gave to the San Diego Union Tribune newspaper, Stein paraphrased himself as writing: "I say screw Obama. I will not follow orders given by him to me."
He later removed the comments and said he meant to refer only to unlawful orders.
Stein, who was supported by a coalition of attorneys who argued that his remarks were protected by the First Amendment of the U.S. Constitution, had asked a federal judge to block the Marines from taking disciplinary action against him.
But U.S. District Judge Marilyn Huff refused to intervene, saying the military had the discretion to discipline Stein after he stated he would not follow all the orders of the president.
Huff said Stein had also criticized Obama in a post on the military's internal network for meteorological and oceanographic information.
She said that message read: "As an active-duty Marine, I have sworn to defend the Constitution against all enemies foreign and domestic. Obama is the economic enemy, the religious enemy, the domestic enemy."
Stein has served nearly nine years in the Marines, including a tour of duty in Iraq. He was due to re-enlist or end his enlistment at the end of July, according to court documents.
He ran afoul of the Marines in 2010 for expressing his opinion as a member of the armed forces rather than as a civilian on the Facebook page. At the time, the American Civil Liberties Union spoke up in his defense.
Marines and all other military members swear an oath to defend the U.S. Constitution and follow the Uniform Code of Military Justice, which restricts political activities while in uniform.
Off-duty, out-of-uniform actions are far less restricted, but there are limits.
(Reporting by Dan Whitcomb; Editing by Cynthia Johnston and Peter Cooney)
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