Cpl. Stephen Funk is accused of being away without leave for 47 days. During that time Funk came out and said he was opposed to war. He claimed he went AWOL to prepare his arguments for conscientious objector status.
During the time he was absent Funk participated in anti-war protests in the San Francisco area.
Funk's lawyers say he was charged only because he spoke out publicly against the war.
Navy judge John A. Maksym rejected their motion to dismiss the case and denied them access to Marine files on who else may have been absent without leave, or AWOL, and how they were punished.
"A mere statement that the accused believed he was specifically targeted is not sufficient to make a showing of selective prosecution or even to compel this court to mandate additional discovery to advance such a theory," Maksym wrote in his ruling, which stemmed from a pretrial hearing on Monday.
Funk's lawyer, Stephen Collier, said that a Marine sergeant said the Marines wanted to make an example out of Funk, who attended war rallies and criticized certain Marine training methods in the media.
But Maksym said a sergeant who may have made an inappropriate comment would not have the authority to initial court-martial proceedings.
Marine spokesman Capt. Patrick Kerr said Thursday's ruling "reinforced our belief that Funk is guilty of desertion and that we in no way singled him out."
Funk's trial is scheduled to begin Sept. 4
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