Moro National Liberation Front founder Nur Misuari was flown on a government-commissioned plane more than 900 kilometres from his southern jungle stronghold to Manila for the meeting with Duterte at the presidential palace.
"I came here to thank him for restoring my freedom, if only partially," Misuari said.
"Should he need our cooperation in his campaign for peace, you can count on us."
Misuari, 77, had been in hiding since his forces allegedly launched attacks on civilians in the southern city of Zamboanga in 2013, leading to a three-week battle against the military that claimed about 200 lives.
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Misuari, a charismatic scholar, founded the MNLF in 1972 to wage a guerrilla war for a separate Islamic state in the south of mainly Catholic Philippines. Most of the nation's Muslim minority live in the southern region of Mindanao.
The conflict, which also involved other rebel groups, is believed to have claimed more than 120,000 lives and contributed to Mindanao remaining the nation's poorest region.
Misuari signed a peace agreement with the government in 1996 in return for the creation of a Muslim autonomous area of which he became governor.
Misuari allegedly orchestrated the 2013 Zamboanga attacks because he felt the MNLF was being sidelined under the planned MILF peace deal with Aquino.
Duterte is aiming to forge a final peace agreement with both groups, although he has not announced concrete plans on how he would do that or settle their rivalries.
It also remains unclear how many armed followers Misuari still has, and how much control he continues to hold over the MNLF.
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