Following independence, Filipino Muslims continued to resist Manila's rule, leading to widespread conflict in the 1970s.

More immediate causes of insurgency rose out of the increasing lawlessness in the southern Philippines during the late 1960s, when violence associated with political disputes, personal feuds, and armed gangs proliferated. In this climate of civil turmoil, longstanding tensions between Moro and Christian communities escalated. Already in competition over land, economic resources, and political power, the Moros became increasingly alarmed by the immigration of Christians from the north who were making Moros a minority in what they felt was their own land. By mid-1972, partisan political violence, generally divided along religious lines, gripped all of Mindanao and the Sulu Archipelago. After martial law was declared in September 1972 and all civilians were ordered to surrender their guns, spontaneous rebellions arose among Moros, who traditionally had equated the right to carry arms with their religious heritage and were suspicious of the government's intentions toward them.

In its initial phases, the rebellion was a series of isolated uprisings that rapidly spread in scope and size. But one group, the Moro National Liberation Front (MNLF) led by Nur Misuari, managed to bring most partisan Moro forces into the loosely unified MNLF framework. Fighting for an independent Moro nation, the MNLF received support from Muslim backers in Libya and Malaysia. When the conflict reached its peak in 1973-75, the military arm of the MNLF, the Bangsa Moro Army, was able to field some 30,000 armed fighters. The military responded by deploying 70 to 80 percent of its combat forces against the Moros. Destruction and casualties, both military and civilian, were heavy; an estimated 50,000 people were killed. The government also employed a variety of nonmilitary tactics, announced economic aid programs and political concessions, and encouraged factionalism and defections in the Muslim ranks by offering incentives such as amnesty and land. The government's programs, and a sharp decrease in the flow of arms from Malaysia, set back the Moro movement. In 1976 the conflict began to wane.

Talks between the government and the Moros began in late 1976 under the auspices of the Organization of the Islamic Conference, a union of Muslim nations to which the Moros looked for support. The talks led to an agreement between the Philippine government and the MNLF signed in Tripoli that year providing for Moro autonomy in the southern Philippines and for a cease-fire. After a lull in the fighting, the truce broke down in 1977 amid Moro charges that the government's automony plan allowed only token self-rule.

The Moro rebellion never regained its former vigor. Muslim factionalism was a major factor in the movement's decline. Differing goals, traditional tribal rivalries, and competition among Moro leaders for control of the movement produced a threeway split in the MNLF during the late 1970s. The first break occurred in 1977 when Hashim Salamat, supported by ethnic Maguindanaos from Mindanao, formed the Moro Islamic Liberation Front, which advocated a more moderate and conciliatory approach toward the government. Misuari's larger and more militant MNLF was further weakened during that period when rival leaders formed the Bangsa Moro Liberation Organization, drawing many Mindanao Maranaos away from the MNLF, dominated by Misuari's Sulu-based Tausug tribe. The Bangsa Moro Liberation Organization eventually collapsed, giving way to the Moro National Liberation FrontReformist Movement. Moro factionalism, compounded by declining foreign support and general war weariness, hurt the Muslim movement both on the battlefield and at the negotiating table. Moro fighting strength declined to about 15,000 by 1983, and Muslim and government forces only occasionally clashed during Marcos's last years in office.

In keeping with her campaign pledge of national reconciliation, Aquino initiated talks with the MNLF--the largest of the three major factions--in 1986 to resolve the conflict with Muslim separatists. Discussions produced a cease-fire in September, followed by further talks under the auspices of the Organization of the Islamic Conference. In January 1987, the MNLF signed an agreement relinquishing its goal of independence for Muslim regions and accepting the government's offer of autonomy. The Moro Islamic Liberation Front, the next largest faction, refused to accept the accord and initiated a brief offensive that ended in a truce later that month. Talks between the government and the MNLF over the proposed autonomous region continued sporadically throughout 1987 but eventually deadlocked.