By the 1990s, Philippine nationalism had not fully penetrated two regions of the country inhabited by national minorities: the Muslim parts of Mindanao and the tribal highlands of northern Luzon. Some Muslims and hill tribespeople did not consider themselves Filipinos, although they were citizens. MÍÍÍÍuslim separatism has a very long history. The Spaniards, Americans, and Japanese all had difficulty integrating the fiercely independent Moros into the national polity, and independent governments in Manila since 1946 have fared little better (see Marcos and the Road to Martial Law, 1965-72 , ch. 1). The Moro insurgency has waxed and waned but never gone away. Enough Muslims participated in the 1987 elections to elect two of the twenty-four senators, but continuing land disputes were major factors preventing reconciliation between Christians and Muslims in Mindanao. The grievances of tribal groups, such as the Ifugao and Igorot, in northern Luzon were of more recent origin, having been stoked by ill-considered Marcos administration dam-building schemes that entailed flooding valleys in the northern Luzon cordillera where the tribal groups lived. When Aquino came to power, she was confronted with a Moro National Liberation Front demand for separation from the Philippines, and a Cordillera People's Liberation Army allied with the New People's Army. Aquino boldly negotiated a cease-fire with the Moro National Liberation Front, and her constitutional commissioners provided for the creation of autonomous regions in Muslim parts of Mindanao and tribal regions of northern Luzon (see The Moros , ch. 5).

Article 10 of the Constitution directed Congress to pass within eighteen months organic acts creating autonomous regions, providing that those regions would be composed only of provinces, cities, and geographic areas voting to be included in an autonomous region. Congress passed a bill establishing the Autonomous Region in Muslim Mindanao with Cotabato City designated as the seat of government, and Aquino signed it into law on August 1, 1989. The required plebiscite was set for November 19, 1989, in thirteen provinces in Mindanao and the island groups stretching toward Borneo. The plebiscite campaign was marred by violence, including bombings and attacks by rebels. Aquino flew to Cotabato on November 6, 1990, to formally inaugurate the Autonomous Region in Muslim Mindanao. She had already signed executive orders devolving to the Autonomous Region in Muslim Mindanao the powers of seven cabinet departments: local government labor and employment science and technology public works and highways social welfare and development tourism and environment and natural resources. Control of national security, foreign relations, and other significant matters remained with the national government. Because many of the provinces to be included actually had Christian majorities, and because the Moro National Liberation Front, dissatisfied with what it perceived to be the limit 7afations o of the new law, urged a boycott, only four provinces (Tawitawi, Sulu, Maguindanao, and Lanao del Sur) elected to join the Autonomous Region in Muslim Mindanao. Cotabato City itself voted not to join. So, a new capital had to be identified. In 1991 Maranaos, Maguindanaos, and Tausugs were disputing where the capital should be (see fig. 3). Indications were that the government of the autonomous region would not have supervisory power over local government officials.

Congress passed a similar law creating a Cordillera Autonomous Region, but in a referendum held in five provinces (Abra, Benguet, Mountain, Kalinga-Apayao, and Ifugao) on January 29, 1990, autonomy failed in all provinces except Ifugao. The reasons for rejection were thought to be fear of the unknown and campaigning for a no vote by mining companies that feared higher taxation. In 1991 the Supreme Court voided the Cordillera Autonomous Region, saying that Congress never intended that a single province could constitute an autonomous region.

Data as of June 1991