The core issue of the problem in Mindanao is the continuing assertion of the Bangsamoro people for restoration of their independence. Problems of land, mass poverty, neglect and underdevelopment and other social inequities are serious problems that need attention of the national government but it is the issue on the political relationship of the Bangsamoro people with the government that needs serious and immediate attention because aside from its historical roots it is being perceived as the major cause of other social, economic and religious problems (Lingga 2005b).
Before the arrival of the Spanish colonialists the Bangsamoro were already in the process of state formation and governance. In the middle of the 15th century Sultan Shariff ul-Hashim established the Sulu Sultanate followed by the establishment of the Magindanaw Sultanate in the early part of the 16th century by Shariff Muhammad Kabungsuwan. Their experience on state formation continued with the establishment of the Sultanate of Buayan, the Pat a Pangampong ko Ranao (Confederation of the Four Lake-based Emirates) and other political subdivisions. These states were already engaged in trade and diplomatic relations with other countries including China. Administrative and political systems based on the realities of the time existed in those states. In fact it was the existence of the well-organized administrative and political systems that the Bangsamoro people managed to survive the military campaign against them by Western colonial powers for several centuries and preserve their identity as a political and social entity.
For centuries the Spanish colonial government attempted to conquer the Muslim states to subjugate their political existence and to add the territory to the Spanish colonies in the Philippine Islands but history tells us that it never succeeded. These states with their organized maritime and infantry forces succeeded in defending the Bangsamoro territories thus preserving the continuity of their independence. That is why it is being argued, base on the logic that you cannot sell something you do not possess, that the Bangsamoro territories are not part of what where ceded by Spain to the United States in the Treaty of Paris of 1898 because Spain had never exercise effective sovereignty over these areas.
The Bangsamoro resistance against attempts to subjugate their independence continued even when U.S. forces occupied some areas in Mindanao and Sulu. Although at this time the resistance of the Bangsamoro governments was not as fierce as during the Moro-Spanish wars but the combined resistance of group-organized guerrilla attacks against American forces and installations and what remained of the sultans’ military power, compelled the U.S. government to govern the Moro territories separate from other territories of the Philippine Islands. Even individual Bangsamoro showed defiance against American occupation of their homeland by attacking American forces in operations called prang sabil (martyrdom operation).
When the United States Government promised to grant independence to the Philippines, the Bangsamoro leaders registered their strong objection to be part of the Philippine republic. In the petition to the United States President on June 9, 1921, the people of Sulu archipelago said that they would prefer being part of the U.S. rather than to be included in an independent Philippine nation (See Appendix C, Jubair 1999: 293-7). Bangsamoro leaders meeting in Zamboanga on February 1, 1924, proposed in their Declaration of Rights and Purposes that the "Islands of Mindanao and Sulu, and the Island of Palawan be made an unorganized territory of the United States of America" in anticipation that in the event the U.S. would decolorize its colonies and other non-self governing territories the Bangsamoro homeland would be granted separate independence. Had it happened, the Bangsamoro would have regained by now their independence when the United Nations decided in favor of decolonization of territories under the control of colonial powers. Their other proposal was that if independence had to be granted including the Bangsamoro territories, fifty years after Philippine independence a plebiscite be held in Mindanao, Sulu and Palawan to decide by vote whether the territory would be incorporated in the government of the Islands of Luzon and Visayas, remain a territory of the United States, or become independent. The proposed fifty-year period ended in 1996, the same year the MNLF and the Philippine government signed the Final Agreement on the Implementation of the Tripoli Agreement. The leaders warned that if no provision of retention under the United States would be made, they would declare an independent constitutional sultanate to be known as Moro Nation (See Appendix D, Jubiar 1999: 298-303). In Lanao, the leaders who were gathered in Dansalan (now Marawi City) on March 18, 1935 appealed to the U.S. Government and the American people not to include Mindanao and Sulu in the political entity to be organized for the Filipinos.
Even after their territories were made part of the Republic of the Philippines in 1946, the Bangsamoro people continue to assert their right to independence. Congressman Ombra Amilbangsa filed House Bill No. 5682 during the fourth session of the Fourth Congress that sought the granting and recognition of the independence of Sulu. When the bill found its way to the archive of Congress the then provincial governor of Cotabato, Datu Udtog Matalam, issued the Mindanao Independence Movement (MIM) manifesto on May 1, 1968 calling for the independence of Mindanao and Sulu.
When it became evident to the Bangsamoro leaders that it would not be possible to regain independence through political means because of lack of constitutional mechanism, the MNLF was organized to pursue the liberation of the Bangsamoro people and their homeland from the Philippine colonial rule through revolutionary means.
The repressive reactions of the government to a peaceful independence movement and the emergence of anti-Muslim militias that harassed Muslim communities triggered the violent confrontations between the Bangsamoro forces and the Armed Forces of the Philippines (AFP) in Mindanao.