During the administration of President Ferdinand Marcos, political tensions and open hostilities developed between the Philippine government and Moro rebel groups.

[41][46] The Moro insurgency was triggered[47] by the purported Jabidah massacre on March 18, 1968, during which 60 Filipino Muslim commandos on a planned operation to reclaim the eastern part of the Malaysian state of Sabah were said to have been killed.

[citation needed] When the MILF modified its demands from independence to autonomy in the late 2008, a faction led by Ameril Umbra Kato disagreed, eventually forming the Bangsamoro Islamic Freedom Fighters (BIFF) in 2010.

The Americans preferred Christians to become administrators of newly defined townships instead of Lumad and Moro, with environmental degradation resulting from unsustainable population growth (due to the influx of settler migrants) and timber logging.

[67] The active phase of the Moro conflict is attributed to news about the Jabidah massacre in March 1968 – towards the end of the first term of President Ferdinand Marcos.

[68][69][70] A senate exposé based on the testimony of an alleged survivor claimed that at least 11 Filipino Muslim military trainees had been killed in Corregidor by soldiers of the Armed Forces of the Philippines.

[71][43] The trainees had been brought to the island of Corregidor to form a secret commando unit called "Jabidah," which would infiltrate, destabilize, and take over Sabah for the Sulu Sultan who previously owned it.

[74] Both Muslim intellectuals and common people suddenly became politicized, discrediting the idea of finding integration and accommodation with the rest of the country, and creating a sense of marginalization.

[50] According to the official line of the MNLF, it was founded on an ideology of egalitarianism, and is thus intended as a secular movement, unlike the Moro Islamic Liberation Front which would later splinter from its ranks in 1978.

[78] During one of the fiercest battles of the insurgency in 1974, Jolo was extensively damaged and news of the tragedy galvanized other Muslims around the world to pay greater attention to the conflict.

The Ilaga engaged in killings and human rights abuses and were responsible for the Manili massacre of 65 Moro Muslim civilians in a mosque in June 1971, including women and children.

Over time, Fr D’Ambra realised that besides strengthening interreligious ties, the Catholic community also needed a better grounding in the faith, founding the Emmaus Dialogue Movement to address this challenge.

[43] On 9–11 December 1997 the MNLF brought the pagan indigenous Lumad leader Mai Tuan to Tehran to attend the eight OIC Islamic Summit Conference.

[89] In 1991, Abdurajak Janjalani, a former teacher who had studied Islam in the Middle East, formed the Abu Sayyaf Group after reportedly meeting Osama bin Laden in Afghanistan in the 1980s.

[43] During his term, President Joseph Ejercito Estrada declared an "all-out war" against the MILF on March 21, 2000, although a series of negotiations for cessation of hostilities were held.

[84] Apparently, several conflicts in and around Mindanao erupted and clashes between the Philippine military and the rebel groups resulted in substantial loss of life.

During Estrada's term, the rebel groups kidnapped three Italian priests, two of whom were later released and one shot dead;[90][91] seized the municipal hall of Talayan, Maguindanao, and Kauswagan, Lanao del Norte; bombed the RORO ferry M/V Our Lady of Mediatrix at Ozamiz; and took over Narciso Ramos Highway.

[94] In 2004, two members of the Jemaah Islamiyah were arrested, namely Mamasao Naga and Abdul Pata, as they were identified by Fathur Rahman al-Ghozi as responsible for the train bombing.

[96] The Abu Sayyaf then conducted a series of raids, including one at a coconut plantation[100] where the rebel groups hacked the heads of two men using bolo knives.

The owners and a security guard were also held captive and the rebel groups burned down two buildings, including a chapel, a week after the battle in Lamitan.

[104] On June 7, 2002, after a year of the hostages being held captive, a rescue mission was conducted resulting in the deaths of Martin Burnham and a nurse named Ediborah Yap[105] after they were caught in the crossfire.

By this time Nur Misuari ordered his supporters to attack government targets to prevent the holding of elections on ARMM in November 2001, ushering his exit as the governor of the region.

During the term of President Benigno Aquino III, a series of peace talks for the cessation of hostilities was held, including the meeting of MILF Chair Al Haj Murad Ibrahim in Tokyo, Japan which was lauded on both sides.

[115] Also, several areas of Mindanao were bombed in August by the government, and a Filipino businesswoman was abducted in September 2011,[116] who was later freed after the three gunmen were gunned down by the Armed Forces of the Philippines.

In February 2013, two main camps of the Abu Sayyaf group were overrun by forces of the Moro National Liberation Front (MNLF) in its latest offensive in Patikul.

The Zamboanga City crisis erupted on September 9, 2013, when a MNLF faction known by other groups as the Rogue MNLF Elements (RME), under the Sulu State Revolutionary Command (SSRC), led by Ustadz Habier Malik and Khaid Ajibon attempted to raise the flag of the self-proclaimed Bangsamoro Republik at Zamboanga City Hall (which had earlier declared its independence on August 12, 2013, in Talipao, Sulu), and took civilians hostage.

[44] On March 27, 2014, the peace process concluded with the signing of the Comprehensive Agreement on the Bangsamoro between the Government of the Philippines and the Moro Islamic Liberation Front.

[128] On January 25, 2015, the Philippine National Police's Special Action Force (SAF) conducted an operation to capture Abdul Basit Usman and the Malaysian terrorist leader Marwan in Mamasapano, Maguindanao.

[citation needed] The MILF and MNLF have expressed their commitment to peace and in finally ending the 47-year-old insurgency while the offensive against Abu Sayyaf and other splinter groups have continued, with skirmishes in Jolo, Basilan and other parts of Mindanao.

The government used heavy artillery and air strikes to shell Abu Sayyaf and Maute positions while the militant groups resorted to executing captured Christians.