Enter Mindanao – the second-largest island in the Philippines, the heart of an archipelago stretching south toward Borneo and the site of one of the longest religiously framed conflicts in modern history. Not always violent, but never at peace, Mindanao is roughly the size of Greece. It is home to 26.5 million people, representing 24 per cent of the Philippines’ 109 million. The minority Muslim Moro people once made up three-quarters of its population; today, they account for less than a fifth. This is the story of five hundred years. Two gods. One island.
The spread of Islam to Mindanao began in the late fourteenth century, introduced through Arab traders from present-day Malaysia and Indonesia. Prior to Islamic influence, the inhabitants of the region primarily practised local forms of animism, mixed with Hindu–Buddhist beliefs, and predominantly lived in small, autonomous communities. By the sixteenth century, sultanates had been established in Sulu, Lanao and Maguindanao from formerly Hindu–Buddhist rajahnates. Islam expanded and gained a strong foothold throughout Mindanao. Those residing within the sultanates largely converted to Islam, while those who resisted were obligated to pay taxes and tributes. Consequently, Islam grew rapidly in the region. The largest area of Muslim control was the Sultanate of the Maguindanaons, from which the name Mindanao subsequently derived. Cartographic evidence from the seventeenth and eighteenth centuries suggests the term Mindanao was used in this period to refer to the current Mindanao mainland and points to the strong establishment of Islam within the region. Islam spread northwards, making inroads in the Negros, Visayas and Palawan regions, although the main stronghold continued to be in Mindanao.
In the mid-sixteenth century, the Spanish arrived in Mindanao after successfully bringing Cebu under colonial control. In their move to conquer Butuan and the surrounding Caranga region of north-east Mindanao, they discovered a significant Islamic presence. Over time, the Spanish converted a number of tribes to Catholicism, established forts and strongholds and engaged in battles with a number of loosely allied Muslim sultanates until the end of the nineteenth century. While during the course of this time, territory was both won and lost on both sides, the Spanish, although dominant at certain periods, were never able to bring Mindanao under control as they had to other regions of the Philippines.
From Spanish rule to American reforms
Spain sold the entire Philippine archipelago, including Mindanao, to the United States in the 1898 Treaty of Paris for US$20 million. During the Philippine–American War (1899–1902), the Americans initially adopted a policy of non-interference in the Muslim areas of Mindanao and enjoyed peaceful relations with sultanate leaders and local datu chiefs on the basis that their traditional authority be recognised. This changed after the war.
The US introduced various social, political and economic reforms, igniting anger in the region. The creation of provincial and district institutions, the introduction of a public school system, an American-style judicial system, new taxations, the outlawing of slavery and polygamy, and notably the mass migration of Filipino Christians to formerly Muslim majority areas were of particular dissatisfaction to traditional leaders, who felt their rights, freedoms and general way of life were being eroded.
The Moro Rebellion (1899–1913) saw the beginnings of armed resistance against the US military and supporting Filipino forces, whose clear military advantage was reinforced by an aggressive exploitation of cultural taboos. The most notorious practice involved wrapping dead Moro fighters in pigskins and stuffing their mouths with pork, an ‘unspeakable defilement with an unclean animal’, as Rear Admiral D.P. Mannix III (1911–1997) recorded in his diary, believed to bar them from paradise. Even so, much like the Spanish before them, the Americans were not able to bring the region under full control, and Moro insurrection persisted so that, at best, only quasi-control was achieved. A tenuous equilibrium lasted until the Second World War, when the Japanese invasion of Mindanao confronted the Moros with a new enemy.
The Japanese forces were faced with fierce Moro resistance and suffered an unanticipated number of casualties, most of them the result of ambushes. While they sometimes found themselves fighting Japanese, American and Filipino forces all at once, the Moros focused most of their efforts on driving out the Japanese. Temporary truces with US and allied Filipino units, notably including an arrangement under which the Moro leader Datu Pino supplied pairs of Japanese ears in exchange for bullets and cash from US Colonel Wendell Fertig, allowed the Moros to secure weapons and concentrate their attacks to the benefit of all parties involved. The Moros remained active against the Japanese even after the Battle of Mindanao (10–15 August 1945), when US forces, assisted by various Filipino guerrilla groups, including Moro fighters, finally brought organised Japanese resistance on the island to an end.
In 1946, the Treaty of General Relations provided recognition of the independence of the Republic of the Philippines, and relinquished American sovereignty over the archipelago. Subsequently, the pace of migration to Mindanao accelerated, encouraged by government-sponsored resettlement programmes launched in the 1950s and 1960s. The purpose of these state initiatives was to ease the pressure for agricultural land and the ensuing related conflicts in the northern regions, particularly in Central Luzon, resulting from a swelling postwar population. Another intention was to exploit the vast wealth of natural resources for the purposes of national development. According to census enumerations from 1948 and 1960, the population of Mindanao increased from less than three million to slightly over five million, giving the island more than double the population growth of the national average, with net migration accounting for over half of the population growth. According to a 2005 Philippine Human Development Report (PHDR), ‘The original Moro peoples have been reduced from 76 percent of the population at the turn of the century to 18 percent at its end.’ Inevitably, this resulted in the dispossession of substantial belts of land held by Moros and indigenous groups. In the late 1960s and 1970s, the situation escalated. With land on the island becoming increasingly scarce, rising tensions fuelled by centuries of mistrust between Christian Filipinos and Moros, plus ruthless discrimination by the Marcos dictatorship, created fertile grounds for an armed Moro uprising.
The birth of Moro separatism
The Jabidah Massacre of March 1968 is considered the catalyst for the modern separatist movement. Purportedly, at least twenty-eight young Moro military trainees were murdered by their superiors to prevent them from leaking information that their training was to infiltrate Sabah, Malaysia and incite instability and unrest among the people. The Philippine government has a long-standing claim over Sabah due to it once being part of the Sulu Sultanate before British annexation in the nineteenth century. The massacre triggered a diplomatic incident from an outraged Malaysian government. Following the subsequent furore, in May of the same year, a collection of Moro leaders, headed by Datu Udtog Matalam (1892–1982), established the Mindanao Independence Movement (MIM) with the intention of forming a separate Moro nation. In 1969, widespread support for Moro separatism coalesced when Chairman Nurullajah (commonly abbreviated to ‘Nur’) Misuari founded the Moro National Liberation Front (MNLF), a revolutionary group aiming to carve out an independent Moro state from Mindanao. Interestingly, before founding the MNLF, Misuari had been a student activist at the University of the Philippines, where he moved in leftist circles alongside future leaders of the Maoist-inspired Communist Party of the Philippines (established in 1968) and the New People’s Army (founded in 1969), organisations that emerged at roughly the same time as the MNLF.
In 1989, three years after the Marcos regime was overthrown, the Aquino government created the Autonomous Region of Muslim Mindanao (ARMM). Despite this, unrest and conflict continued partly due to ideological reasons and largely because of the failure of the region to gain any real or meaningful autonomy. In 1996, after another protracted conflict, the Final Peace Agreement between the government and the MNLF was signed, yet once again this did not appease certain groups within the MNLF who had broken away to form the Moro Islamic Liberation Front (MILF). As their name suggests, their demand was not autonomy, but an independent Islamic state.
The ARMM, for various reasons, failed to alleviate poverty or bolster economic development; the governing body was ‘too weak to address even basic human development needs’, and thus sporadic outbreaks of violence appeared through the end of the last century, with MILF emerging as the more powerful faction. In an attempt to contain the threat, the Philippine government declared ‘all-out war’ against the MILF in June 2000 and again in 2003. Since then, a fragile ceasefire has been held and broken multiple times. Recurring conflict has damaged the social fabric of Mindanao, displacing entire communities and resulting in extensive infrastructural damage. While the MILF are now the dominant Muslim authority in Mindanao, the organisation has fractured into several internal groups with different leadership. Several splinter groups have emerged from the organisation largely in retaliation for peace talks and coordinated planning between the MILF and the government to establish greater autonomy for the region.
Corruption, political dynasties, clan feuding, militias, left-wing insurgency groups, extremist splinter factions, gangs, drug cartels and global terrorist networks complicate the picture further, igniting intermittent conflict throughout the region. Since 2003, there have been numerous acts of terrorism and incidents of violence, including shootings, bombings, hostage-taking and kidnap situations, and even military assaults on towns and cities.
In 2017, the terrorist group Islamic State (IS) began in earnest with their expansion into the Philippines. IS-affiliated Abu Sayyaf and the Maute Group fighters (plus other smaller jihadist groups), comprising a force of former MILF guerrillas and foreign fighters, attacked the city of Marawi under the IS banner. The Siege of Marawi was a five-month-long armed conflict, the longest urban battle in the modern history of the Philippines. The damage to the city’s infrastructure and the displacement of residents have been an expensive cost to bear. The government estimates that about 200,000 residents were displaced and that 95 per cent of the structures within the 4 square kilometres of the ‘most affected area’ were heavily damaged or completely collapsed. At least 3,152 buildings were destroyed, and 2,145 buildings were partially to heavily damaged due to the fighting. While the government forces were successful in expelling IS from the city, the military is continually on high alert, conducting skirmishes throughout the region.
Autonomy promised, autonomy delayed
In February 2019, the ARMM formally transferred power to the newly formed Bangsamoro Autonomous Region in Muslim Mindanao (BARMM). An eighty-member Bangsamoro Transition Authority (BTA), composed of forty-one members from the MILF and thirty-nine from the government, was mandated to govern the BARMM during a transitional period that was initially meant to last until 2022, when the first Bangsamoro parliamentary elections were supposed to be held. However, these inaugural elections were later postponed by national legislation, first moving them to 2025 and then resetting the deadline to no later than 31 March 2026, on the grounds that the BARMM’s institutions and legal framework were not yet fully prepared for credible polls, and that more time was needed to pass priority laws, strengthen core ministries and stabilise security conditions before holding genuinely representative elections. Unsurprisingly, repeated delays have themselves become a source of frustration and uncertainty. That deadline passed too. In March 2026, Marcos signed a fourth postponement into law, resetting the vote to 14 September 2026 – the first parliamentary election in the region’s history, more than four years late.
For some, this new regional autonomous government is the latest and most ambitious effort to end the insurgency by recognising the Moro community’s right to self-determination. Many argue that it not only offers the greatest chance of finally delivering a political solution, but also of degrading the mutually beneficial ties between Moro insurgent and terrorist groups, and other regional and global terrorist networks.
In theory, the new expanded BARMM will have a much wider range of powers and fiscal capabilities than the ARMM. However, some have their reservations. The same issues that undermined the effective implementation of the ARMM haven’t gone away. The most obvious problems are the substantial pockets of local Muslim opposition to the new BARMM, serious questions about the capacity of Muslim Mindanao as a whole and the MILF to satisfy governance demands, and the national government’s level of support.
There are serious concerns that history will merely repeat itself. The decades of negotiation between Manila and the MNLF, which led to the creation of the ARMM, significantly weakened the MNLF’s claims to represent the Moro community. Many saw the ARMM as an agreement between the MNLF, at the time led by Nur Misuari, and Manila, and not as an inclusive regional autonomous government for all. This exclusivist view was further cemented as Nur Misuari became ARMM governor after the first elections were held.
The BARMM will be met with the same criticism by its opponents in Mindanao as an agreement between the MILF and Manila. Efforts to include Nur Misuari’s Sulu-based MNLF faction in the negotiations have widely failed, contributing to a greater sense of exclusion. Many interpret the 2013 Siege of Zamboanga City as a reaction against the negotiations between the national government and the MILF. Strikingly, this episode remains relatively obscure in broader public memory, despite the massive destruction it caused: over 10,000 homes destroyed, some 120,000 people displaced and a significant loss of life that left a deep imprint on the city’s long, uneven recovery.
In 2015, the Bangsamoro Islamic Freedom Fighters (BIFF), a MILF splinter faction, took responsibility for the Mamasapano Massacre – the group opposed negotiations between the MILF and Manila. Similarly, the aforementioned IS-affiliated Abu Sayyaf and Maute Group that led the Siege of Marawi in 2017 are also opposed to the MILF and its negotiations with Manila. Despite the invocation of martial law across Mindanao (in reality this is not applied strictly to all areas), violent attacks persist and pose an ongoing challenge to the peace and stability of the region.
It is hardly surprising that these conflict-affected areas have the highest levels of general poverty and the lowest levels of human development in the Philippines. Both the human and financial costs of the conflict have been vast. Conservative estimates, with emphasis on conservative, say that the conflict has directly claimed over 120,000 lives with an economic cost of over US$10 billion.
Religion runs like a thread through Mindanao’s history, but it is only one strand in a knot of land disputes, state-building failures and global geopolitical currents. Islam arrived centuries before Spanish Catholicism, shaping sultanates and law, while later waves of Christian migration turned many areas into Muslim minorities, with predictable resentment. This gradual demographic inversion hardened identities, made everyday competition feel existential and turned religious affiliation into a convenient shorthand for a deeper struggle.
The resulting landscape is not a simple clash of faiths, but an archipelago of overlapping religious and political projects. In some communities, Christians and Muslims have long histories of trade, intermarriage and practical coöperation; in others, memories of massacres, broken promises and forced displacement mean that churches and mosques stand as quiet markers of contested history. That tension helps explain why some Moro groups have backed gradualist autonomy, others push for full independence and a smaller subset has been drawn into explicitly transnational jihadist narratives that reframe local grievances as part of a much larger cosmic struggle between Islam and the west.
Seen from that angle, Mindanao is not just a distant theatre, but a microcosm of the fraught relationship between the world’s two largest Abrahamic religions. Both Islam and Christianity in the Philippines are capable of inspiring coexistence and peace-making. Many of the most effective grassroots initiatives are faith-led, yet both have also been mobilised to justify violence. It would seem as though religious identity becomes the language through which historical injustice, state neglect and global ideological currents are expressed.
