Despite questions on the region's constitutionality, as it would have adopted a parliamentary system in an area of a country with a presidential system of government, no judicial ruling was made against the organic law and consequently a two-part plebiscite was held: one by ARMM citizens determining whether to dissolve the ARMM and immediately replace it with the Bangsamoro and, following the approval on the first part,[9][10][11] a second part taken by neighboring municipalities and barangays in the provinces of Lanao del Norte and Cotabato regarding their cession to the Bangsamoro region.

[12][13][14][15] As a result of the second part of the plebiscite, 63 barangays of Cotabato province were handed over to the Bangsamoro government, adding to the autonomous region's territory.

[17] Currently in transition until 2025, the Bangsamoro government has been considered a testing ground for the wider debate on constitutional reform and federalism in the Philippines.

The westernmost and west-central areas have been the traditional homeland of Muslim Filipinos since the 15th century, even before the arrival of the Spanish, who began to colonize most of the Philippines in 1565.

It was not until the last quarter of the 19th century that the Sultanate of Sulu formally recognized Spanish suzerainty, but these areas remained loosely controlled by the Spanish as their sovereignty was limited to military stations and garrisons and pockets of civilian settlements in Zamboanga and Cotabato,[20] until they had to abandon the region as a consequence of their defeat in the Spanish–American War.

The violent armed struggle against the Japanese, Filipinos, Spanish, and Americans is considered by modern Moro Muslim leaders as part of the four centuries long "national liberation movement" of the Bangsamoro (Moro Nation), although the term is only used in mainland Mindanao as those in the Sulu archipelago had a much distinct culture.

[21] The 400-year-long resistance against the Japanese, Americans, and Spanish by the Moro Muslims persisted and morphed into a war for independence against the Philippine state.

The violence and brutality of the Spaniards in their attempts to suppress the Moro groups have resulted in killing numerous families and setting villages on fire.

This US-led Homestead Program, which was later continued or copied by Philippine administrations after independence, is therefore often cited as one of the root-causes of what would later become the larger Moro conflict.

Under pressure to resolve agrarian unrest in various parts of the country and noting that Mindanao was rich in mineral resources and weather favorable to agriculture, later Philippine presidents continued the promotion of migration which the American colonial government began in 1903.

[25] The best lands in Mindanao were given to settlers and owners of corporate agriculture, while most development investments and government services were offered to the Christian population.

[28] The Philippine government did not immediately recognize Islamic laws which resulted in the system of education and the socioeconomic development of the Muslims.

The military began training them on the island of Corregidor to form a secret commando unit called Jabidah, which would destabilize and take over Sabah.

[36] The advocacy of Ansar El Islam would, later on, inspire the creation of the Moro National Liberation Front (MNLF) and the MILF.

[40] The MIM did not last long because Datu Udtog Matalam negotiated with Marcos and accepted a post in his cabinet, but many of its members broke away and became the main force of the MNLF.

[41] On September 23, 1972, Ferdinand Marcos announced that he had placed the entirety of the Philippines, including Muslim Mindanao, under martial law.

While Datu Udtog Matalam's MIM was already defunct, one of its former members, Nur Misuari, established the MNLF a month after the declaration of Martial Law, on October 21, 1972.

[42] On December 23, 1976, the Tripoli Agreement was signed between the Philippine government and the MNLF with the deal brokered by then-Libyan leader Muammar Gaddafi.

Salamat formed a splinter faction along with 57 other MNLF ground commanders, which then became the Moro Islamic Liberation Front (MILF).

[46] A year after Marcos was ousted from power during the People Power Revolution, the government under President Corazon Aquino signed the 1987 Jeddah Accord in Saudi Arabia with the MNLF, agreeing to hold further discussions on the proposal for autonomy to the entirety of Mindanao and not just the thirteen provinces stated in the 1976 Tripoli Agreement.

Shortly thereafter, the government held only four provinces as only Lanao del Sur, Maguindanao, Sulu and Tawi-tawi voted to be included in the ARMM.

In 2012, Aquino announced intentions to establish a new autonomous political entity to be named Bangsamoro to replace the ARMM, which he called a "failed experiment".

[49] Under his administration, a draft for a Bangsamoro Basic Law (BBL) was formulated but failed to gain traction to become law, owing in part to the Mamasapano clash that occurred in January 2015[43] that involved the murder of 44 mostly-Christian Special Action Force (SAF) personnel by allegedly combined forces of the MILF and the Bangsamoro Islamic Freedom Fighters (BIFF) after an operation to kill Malaysian militant Zulkifli Abdhir, known by the alias "Marwan".

Despite voting against inclusion, Sulu was still included in the Bangsamoro region due to rules stated in the BOL, sparking outrage from residents.

[55][56] With the ratification of the BOL following the plebiscite on January 21, 2019, the abolition process of the ARMM began, paving way for the setting up of the Bangsamoro autonomous region.

The second part of the plebiscite held on February 6, 2019, expanded the scope of the future Bangsamoro region to include 63 barangays in North Cotabato.

Murad Ebrahim is the current chief minister, who was appointed by the former Philippine president Rodrigo Duterte, on an interim basis.

[81] Under the BOL, the Bangsamoro Parliament serves as the legislature of the autonomous region, mandated to have 80 deputies and is led by the speaker.

The Bangsamoro justice system also recognizes traditional or tribal laws but these would only apply to disputes of indigenous peoples within the region.

The Sulu archipelago region includes the Turtle Islands Wildlife Sanctuary (a UNESCO tentative site), Bongao Peak, and the Basilan Rainforest.