In a statement, the Corps said Captain James Clement "will be tried for dereliction of duty and conduct unbecoming an officer and a gentlemen for failing to stop the misconduct of junior Marines."
He is accused of failing to prevent men under his command of desecrating the bodies of three Afghans, in a case that dates back to July 27, 2011, during an operation against the Taliban insurgency in Afghanistan's Helmand province.
A few days later, a 21-year-old Afghan soldier opened fire on some French soldiers who were training Afghan troops, later saying it was in retaliation for the desecration. Five French soldiers were killed and 15 wounded.
All five of the Marines belong to an elite unit of snipers. One, Staff Sergeant Joseph Chamblin, was jailed for 30 days, fined and demoted after pleading guilty to participating in the video.
Others involved in the case have faced administrative sanctions.