The judge, Marine Maj Nicholas Martz, ruled that Cpl Wassef Hassoun was guilty of deserting for the 2004 and 2005 disappearances. Hassoun was also convicted of causing the loss of his service pistol.
Sentencing is expected later this week after more witnesses are called. A spokesman for the US Marines, Captain Stewart Coles, said in a release that Hassoun faces a maximum penalty of seven and a half years in prison, reduction in rank and a dishonourable discharge.
Had he been convicted of all charges and specifications, he could have been sentenced to a maximum of 27 years in prison.
Hassoun was found not guilty of a theft charge related to his pistol, and his conviction for losing the pistol represents a lesser offense included under the military's destruction of property charge.
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Hassoun was also found not guilty on one of three specifications related to the desertion charge.
They displayed quotes during opening statements attributed to Hassoun: "I'll leave and go to Lebanon. I'm not kidding."
They said he was unhappy with how US servicemen treated Iraqis during interrogations and that he was upset that training and a second deployment to Iraq kept him from being with a woman with whom he'd entered an arranged marriage.
Defense attorneys maintain that Hassoun was kidnapped by insurgents in 2004. They argued that the case against the Muslim serviceman began with a "rush to judgement" by Navy investigators after suspicious comrades told investigators about comments Hassoun made about the conflict between his native Lebanon and Israel.