In total, nine of the elite troops had been arrested since Thursday, with the Royal Military Police (RMP) seizing one marine on suspicion of murder on Friday and another on Saturday.
Four have since been released without charge, pending further inquiries.
A statement from the MoD released yesterday said: “The RMP has referred the cases of the remaining five Royal Marines to the independent Service Prosecuting Authority (SPA).
“Following direction from the SPA these marines have now been charged with murder and they remain in custody pending court proceedings.”
The soldiers, believed to be members of 3 Commando Brigade, were arrested in connection with a death that occurred while they were based in Helmand.
The incident has been described as “an engagement with an insurgent”, with no civilians involved.
During a six-month tour of duty from April to October last year, seven servicemen from 3 Commando Brigade were killed in action.
The arrests are thought to be the first time UK servicemen have been held on suspicion of such charges during the conflict and have prompted a furious reaction with tens of thousands of people backing a Facebook group in support of the marines.
But senior Army sources last night told the Yorkshire Post that any sign the MoD was not investigating incidents fully could have dire implications, putting lives at risk.
Defence Secretary Philip Hammond said he was determined the rules of engagement were followed in Afghanistan.