The Marine Corps announced the criminal charges Monday against Staff Sgt. Joseph W. Chamblin and Staff Sgt. Edward W. Deptola, both based at Camp Lejeune, N.C.
Three other Marines were given "non-judicial administrative punishments."
These can include, a reprimand, reductions in rank, forfeiting pay, extra duties or being restricted to a military base.
The unit, which is based at Camp Lejeune, North Carolina, deployed last February or March and returned in September or October.
The incident allegedly occurred in July 2011 in the Helmand Province of Afghanistan.
After returning to Camp LeJuene the Marine reportedly began passing the video around as a war trophy.
The video shows four men dressed in Marine combat gear urinating on what appeared to be the dead bodies of three men on the ground in front of them.
One of the men says, "Have a great day, buddy." A voice asks, "You got it on the video?" to which another voice responds, "Yeah." Another jokes, "Golden, like a shower."
"I have seen the footage, and I find the behavior depicted in it utterly deplorable," U.S. Defense Secretary Leon Panetta said in a statement. "I condemn it in the strongest possible terms."
Lt. Gen. Adrian Bradshaw, deputy commander of ISAF, called the actions on the video "disgusting."
"Any acts which treat the dead, enemy or friendly, with disrespect are utterly unacceptable and do not represent the standards we expect of coalition forces," Bradshaw said in a video statement. He said he was speaking on behalf of Allen, who is out of the country.