Nur Misuari, leader of the Philippine group Moro National Liberation Front (MNLF), faces charges of rebellion and violating human rights after a deadly three-week standoff in the country's south between government troops and Muslim fighters who held scores of people hostage.
Peter Medalle, the regional state prosecutor, said on Thursday that authorities had filed the charges against Misuari and 80 of his followers.
Rebellion is punishable by life imprisonment.
More than 200 people were killed and nearly 10,000 houses were burned in the fighting that followed the alleged MNLF attempt to storm Zamboanga City Hall on September 9.
"We have gathered affidavits linking Misuari to the said attack," Senior Superintendent Edgar Danao, a senior police investigator, said.
Misuari is believed to be hiding in southern Philippines.
Police have so far filed complaints for rebellion and other criminal cases against 224 MNLF leaders and followers, most of them now detained, Chief Inspector Ariel Huesca, the regional police spokesman, said.
State prosecutors will evaluate the evidence submitted by police, then decide whether to bring charges in court.
The MNLF was founded by Misuari in the early 1970s to fight for minority Muslim self-rule in the predominantly Catholic nation.
It signed a 1996 peace agreement then accused the Philippine government of failing to honour it.
Misuari's armed followers led a similar attack in 2001, during which they also seized civilian hostages.
He was charged with rebellion, but was acquitted for lack of evidence.
Muslim rebels have been fighting since the 1970s for an independent or autonomous homeland in the south of the mainly Catholic Philippines. An estimated 150,000 people have died in the conflict.
The MNLF signed a peace treaty in 1996 that granted limited self-rule to the south's Muslim minority.
However, the group opposes a planned final peace deal between the government and the remaining major Muslim rebel group, the 12,000-strong Moro Islamic Liberation Front.
Misuari apparently fears the proposed peace deal would sideline him and his group.