The biggest Muslim rebel group in the Philippines signed an historic pact on Thursday to end one of Asia's longest and deadliest conflicts, promising to give up their arms for an autonomous homeland.

Following four decades of fighting that has claimed tens of thousands of lives, the Moro Islamic Liberation Front (MILF) signed the peace deal with President Benigno Aquino's government at a high-profile ceremony in Manila.

"The comprehensive agreement on Bangsamoro is the crowning glory of our struggle," MILF chairman Murad Ebrahim said at the signing ceremony, using a local term that refers to a Muslim homeland.

"With this agreement the legitimate aspirations of the Bangsamoro and the commitment of the government of the Philippines to recognise those aspirations are now sealed."

The pact makes the MILF and the government partners in a plan to create a southern autonomous region for the Philippines' Muslim minority with locally elected leaders by mid-2016.AFP