In the middle of the 14th cent. Islam spread from Malaya and Borneo to the Sulu Archipelago, and from there to Mindanao. The arrival of the Spanish in the late 16th cent. united the various Muslim groups in a war against the conquerors that lasted some 300 years. The Moros likewise resisted American domination; fighting between U.S. garrisons and Muslim groups occurred early in the 20th cent.

Although many of the Philippine Islands suffered extensive damage in World War II, Mindanao emerged relatively unscathed. As the chief frontier left in the difficult reconstruction years, it was the object of government colonization projects. During the 1960s it experienced a phenomenal population increase and very rapid development. These changes brought serious problems. The native Moros, finding themselves outnumbered and in many cases pushed off their lands, retaliated with terrorist activities. When the Philippine army attempted to restore order, fierce fighting often resulted. In 1969 and the early 1970s several thousand people were killed and hundreds of villages were burned.

In 1971 anthropologists reported the discovery of the Tasaday, whom they portrayed as a Stone Age people inhabiting caves in Mindanao's rain forest and threatened by the encroachment of lumbering, mining, and ranching interests. By the mid-1980s, when evidence had emerged indicating that the Tasaday were perhaps a division of a neighboring, comparatively sophisticated people, there arose a suspicion that the Tasaday phenomenon was a hoax, possibly instigated by the Marcos government.

In 1976 the Philippine government pledged to grant autonomy to several provinces in Mindanao. It was not until 1990, following a plebiscite boycotted by many Muslims and dominated by Christian majorities in a number of provinces, that the Autonomous Region in Muslim Mindanao (now consisting of the Mindanao provinces of Maguindanao and Lanao del Sur and the Tawi-Tawi, Sulu, and Basilan provinces in the Sulu Archipelago) was granted partial autonomy. Muslim discontent with partial rule persisted, and unrest and violence continued through 1990s. A 1996 agreement led to peace with one group of rebels and the expansion of the autonomous region in 2001. Negotiations continue with another Moro group, but they and fundamentalist Islamic guerrillas have continued fighting and terror attacks. An agreement reached (Nov., 2007) in principle with the second Moro group collapsed after it was challenged in court (and subsequently declared unconstitutional). Significant fighting broke out beginning in Aug., 2008, between government forces and some Moro rebels. Government military operations continued until mid-2009. Peace talks resumed late in 2009, but subsequently there were occasional outbreaks of fighting. In 2012 the government and the second Moro group signed a framework peace agreement that would create a new autonomous region superseding the current one.