Not to be confused with the Great War in Mindanao and Sulu that lasted from 1521 to 1900

War in Mindanao and Sulu
Perang Di Mindanao dan Sulu
Fighters of the Mindanao Free Army in Jolo celebrate a victory over the Filipino army
Date 1949-1967
Location Mindanao, Sulu Archipelago, Palawan, Balabac, Bataraza, Cebu
Status - Both sides claim victory
- Malaysia invades Mindanao and Sulu
Flag of Mindanao Republic of Mindanao
Late 19th Century Flag of Sulu Kingdom of Sulu
Flag of the Philippines Philippines
Flag of the United States United States
Flag of Mexico Mexico
Commanders and leaders
Flag of Mindanao Gumbay Piang
Flag of Mindanao Salipada Pendatun
Flag of Mindanao Muhsinal Islam
Flag of Mindanao Juan Sagun
Flag of Mindanao Lao Xing-Tai
Flag of Mindanao Ahmad Bashar
Flag of Mindanao Sindhi Sidartha
Flag of Mindanao Christopher Francis
Late 19th Century Flag of Sulu Jainal Abirin
Late 19th Century Flag of Sulu Mohammad Kiram I
Late 19th Century Flag of Sulu Abang Hashim
Late 19th Century Flag of Sulu Karim Salamat
Flag of the Philippines Elpidio Quirino
Flag of the Philippines Ramon Magsaysay
Flag of the Philippines Carlos P. Garcia
Flag of the Philippines Diosdado Macapagal
Flag of the Philippines Ferdinand Marcos

The War in Mindanao and Sulu (Filipino: Laban sa Mindanao at Sulu, Malay: Perang Di Mindanao dan Sulu, Spanish: Guerra en Mindanao y Sulu) also known as the Mindanao Independance Struggle (Malay: Perjuangan Merdeka Mindanao) was an armed struggle between the Mindanao Free Army and Royal Sulu Army against the Philippine Armed Forces for control of the islands of Mindanao, the Sulu Archipelago, Palawan and parts of Cebu that lasted from 1949 to 1967 and concluded with the Malaysian invasion of Mindanao. It was often referred to by Moro nationalists and historians as the successor to the 400-year war of a similar name "The Great War in Mindanao in Sulu " that lasted from 1521 to the late 1800s between the kingdoms of Mindanao and Sulu Archipelago against the Spanish Empire.

It started in 1949, when Moro nationalist leader Gumbay Piang  proclaimed independence for Mindanao from Philippine rule, the same time his ally Jainal Abirin was crowned the Sultan of Sulu. Piang dreamed of a united and free Mindanao in which both Moros and Lumads (non-Muslim natives) could fight together. This resulted in a military response from the Philippine government, by sending forces to Mindanao and Sulu, thereby starting the armed struggle for independence among the peoples of Mindanao and the Sulu Archipelago.

Piang united both the Muslim and non-Muslim natives of the island.

Due to incompentency in leadership witin the Filipino forces, the Mindanao Free Army found itself successfully holding off and repelling the Filipino forces through three presidencies. The MFA defeated the Filipino army in many key cities and regions in Mindanao, including Maguindanao, Marawi City, Zamboanga City and Jolo. Due to these Moro victories, Gumbay Piang, the president of Mindanao and Sulu, became complacent, and led to the failed invasion of Palawan, in which the Mindanao Free Army was defeated by the Filipino forces. The MFA also claimed Cebu, seeing the island as historically important to the Moro people, and engaged in limited battles with the Filipino forces in Cebu City. They wanted to occupy Mactan Island, home of Lapu-Lapu, the rajah that slayed the Portuguese conquistador Ferdinand Magellan. Salahuddin attempted to rename Cebu City as Kota Sugbu (its direct ancient Malay-translated name) or back to its ancient name Singhapala.  In 1955, the Kingdom of Sulu joined the Mindanao Republic, and thus, the former Royal Sulu Forces was integrated into the Mindanao Free Army.

Over the years, the Mindanao Free Army grew, eventually getting ethnic Chinese-Filipinos and Visayan Christians and Hindus/Buddhists in Mindanao to become fighters for the MFA rather than just Moro and Lumads. Salahuddin was later successful in recruiting Indonesians.

Still, for much of the de facto Republic of Mindanao's existance, the Mindanao Free Army continued to hold off Filipino incursions into the south, nearly forcing the Philippine government to submit and grant Mindanao its independence. The Mexican government, sent military aid to the Philippines, however this only worsened the situation, and fueled the MFA with even more motivation. Across Mindanao, there were Mexican flag-burning events with demonstrators carrying signs with anti-Mexico slurs and slogans. This led to the Mexican Embassy Incident of 1961, in which Moro communities and MFA sympathizers in Manila surrounded the Mexican embassy and threw stones at it. In addition, this would begin the "Mexican witch hunt" across the Philippines, in which Moros and Filipino sympathizers would discriminate overseas Mexicans, or Filipino Mestizos with Mexican descent. This would end with the rule of Ferdinand Marcos, who had purged the army of incompetent leaders and replaced them with better leaders, trained by Americans, getting the United States involved on the Philippine side. Thus in 1967, the Mindanao Free Army, battered, was on the brink of total defeat and contemplated a surrender with the Filipino government.

Meanwhile in Malaysia, President Tunku Abdul-Rahman used this as an oppurtunity to invade and annex Mindanao and the Sulu Archipelago, as part of his "United Malaysian Commonwealth" vision. When word leaked to the Moro and Lumad leaders, they knew they could not afford to fight another war, having been too exhausted and battered with the war against the Philippines.

Therefore, knowing that a Malaysian occupation would put the Moros under a Muslim government, the Moros agreed to support a Malaysian invasion of Mindanao. Afterwards, Malaysia invaded Mindanao and the Sulu Archipelago, thus starting the Malaysian-Philippine War. Those who served in the MFA would be incorporated into Moro and Lumad units of the Malaysian Armed Forces.

Other countries involved included the People's Republic of China, who while announcing no official support for either side, evidently sided with the Mindanao Free Army with speculations of the Chinese-controlled illicit weapons trade being supported by the Chinese government. Indonesia was also heavily involved, while the Indonesian government wished for peace and the best-outcome for the Philippines, its government declared a state neutrality. The Mindanao Free Army however was able to recruit many Indonesians. This was due in part that Sukarno supported the Moro nationalists, but at the same time, viewed the Philippines as one of Indonesia's most important "friends" and allies in Southeast Asia. Although Indonesia would align itself with the Philippines during the war with Malaysia. 

While the United Kingdom offered protectorate status to the Kingdom of Sulu, it also wished to maintain a state of neutrality siding with neither the Filipinos or the Moros. 

However, the Mindanao Constabulary, the branch of the Philippine National Constabulary operating in Mindanao and Sulu, is considered a succeeding descendant of the Mindanao Free Army. Under Corazon Aquino's presidency, she also allowed certain fighters from the Mindanao Free Army to be considered Filipino veterans.

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