Corporal Wasif Ali Hassun, a Lebanese-born Arabic translator, disappeared from a marine base near Falluja on 21 June only to surface 19 days later in Lebanon where he turned himself in to US authorities.
During his disappearance, Aljazeera aired a videotape that showed Hassun as a captive of masked, armed fighters.
Initially listed as a deserter, his status was changed to captured after the video was aired.
"The US marines have charged Corporal Wasif Ali Hassun with desertion following a five-month investigation into his disappearance from a US military camp in Iraq in June," the marines said in a statement on Thursday.
Charges of desertion, wrongful disposition of military property
and two counts of larceny or theft were slapped on Hassun on Thursday after the navy's criminal investigative services completed their investigation of the disappearance.
Hassun was accused of stealing his 9mm service pistol and a government vehicle.
An Article 32 investigation, the military's equivalent to a grand jury investigation, will consider whether the evidence supports referring the case to trial by a military court.
Aljazeera aired a tape showing
Hassun held by masked fighters
Hassun, 24, enlisted in the marines in January 2002 and worked as an Arabic translator in Iraq.
On his return to the US in July, Hassun denied reports that he had deserted his post.
"I was captured and held against my will by anti-coalition forces for 19 days," he said from the Quantico marine base near Washington.
"This was a very difficult and challenging time for me," he added. A marine spokesman would not comment on the investigation's findings.
Hassun is assigned to the 4th Marine Expeditionary Brigade at Camp Lejeune, North Carolina, where he now works as a driver.
"Hassun is here in Camp Lejeune. He's going about his normal duties," said Major Matt Morgan. "He has not been arrested or otherwise detained."