Under the leadership of Fidel V. Ramos, the government and MNLF signed the final peace agreement in Jakarta, Indonesia, in 1996.  He allowed qualified MNLF members to join the Philippine Armed Forces and the Philippine National Police and founded the Southern Philippines Council for Peace and Development, dominated by the MNLF. Misuari then ran for governor of the ARMM.  In 1997, Ramos and Misuari won the peace agreement at the Felix Houphouét-Boigny Peace Prize.  Ferdinand Marcos then implemented the agreement by creating two autonomous regions (instead of one) composed of ten provinces (instead of thirteen). This led to the collapse of the peace pact and the resumption of hostilities between the MNLF and Philippine government forces.   The agreement provided for the creation of an autonomous region of 13 provinces and the cities of Mindanao and Palawan: Basilan, Davao del Sur, Lanao del Norte, Lanao del Sur, Maguindanao, North Cotabato, South Cotabato, Sultan Kudarat, Sulu, Tawi-tawi, Zamboanga del Norte, Zamboanga del Sur – all in Mindanao – and Palawan and its interior towns. The MOA-AD was then declared unconstitutional by 8 to 7 votes. But the Supreme Court also recognized that it was “an essential part” of a series of agreements needed to implement the Tripoli peace agreement signed in 2001 by the government and MILF with grP-MILF. The 2001 Tripoli Agreement cited the 1997 ceasefire agreement the 1976 Tripoli Agreement and the 1996 Jakarta Agreement between the Philippine government and the MNLF, as well as an OIC resolution calling on the government and MILF to “immediately end armed hostilities and continue peace talks to find a peaceful solution to the problem in Mindanao.” That same year, the Moro Islamic Liberation Front, which had separated from the MNLF in 1977, began informal discussions with the Ramos government. However, these were not followed, and milF began to recruit and establish camps and become the dominant Muslim rebel group. Joseph Estrada`s government has called for a firm stance against it; Gloria Macapagal Arroyo tried to sign a peace agreement with him, but it was declared unconstitutional by the Supreme Court of the Philippines.
 After the signing of the Tripoli Agreement, some of the founding members of the MNLF, such as Ustadz Salamat Hashim, decided to create their own group.