Historians have scant knowledge of the pre-Spanish history of the Yakan simply because they have little contact with other ethnic groups. Basilan's nearness to Borneo led to the theory that the Yakan originated from the Dyak, but it is safe to say that Basilan's history is related to that of the Sulu archipelago.
By 1654 there were about 1,000 Christian families living in the island.
By the 1840s, colonial interests other than Spanish focused over western Mindanao, particularly the territories under the Sulu sultanate. The British, French, Germans, and Americans all became interested in these rich islands. In reaction, the Spanish government in 1842 established Fort Isabela in the northwest coast of Basilan. The area then grew into a Christian settlement which also became a trade and commercial center.
Despite such progress in Basilan, the Yakan remained in the interior, hostile to lowlanders. But in the year 1842, a fugitive from Cavite named Pedro Cuevas escaped to Basilan where he fought and killed a Yakan chieftain named Datu Kalun (also spelled Kalung and Kalum). Cuevas then adopted the name of Datu Kalun. The Yakan accepted Cuevas as their leader because he embraced the Yakan religion and way of life, married one of their women, and instituted meaningful sociopolitical changes in their lives. Datu Kalun consolidated the Yakan, led battles against the invading rulers from Jolo, and rid Basilan of pirates and marauders.
In 1844, the French government tried to occupy Basilan, intent on establishing a network of naval stations to protect French trade. The inhabitants of Basilan fought against the French for a year, resulting in a French withdrawal, as formalized in a proclamation dated 5 August 1845. During the same year, a US survey mission studied the potentials of the Sulu archipelago, but American intervention did not start until 1899.
In 1895, the Sultan of Sulu sent his bravest general, Datu Julkanayin, to regain control over Basilan, only to be defeated by Datu Kalun's forces. The ensuing peace encouraged more Christians to settle in Basilan. Thus, the Spaniards now considered Cuevas/Datu Kalun an ally and pardoned him for his earlier offense.
While Zamboanga and Sulu were the centers of Spanish-Muslim hostilities, Basilan inhabitants, especially the Yakan, remained fairly unaffected by the social upheavals. Still, the Yakan were among those natives called Moros by the Spaniards.
The arrival of the Americans in 1899 changed the situation in Mindanao. The American strategy of integration was more acceptable to the Muslims than the Spanish strategy of conversion. The new colonizers were received openly by the Muslim elite. On 19 May 1899, American troops took over the Spanish garrison in Zamboanga, one of the last strongholds of the Filipino revolutionaries in Mindanao. By December 1899, the Americans led by Col. James S. Petit occupied the Spanish naval base of Isabela de Basilan. In Basilan, an old and sickly Datu Kalun (Pedro Cuevas) supported the new colonizers.
Datu Kalun died in Basilan on 16 July 1904 at the age of 58, soon after his first contract with the Americans. His nephew Gabino Pamaran became his successor and adopted the name Datu Mursalun. Mursalun, also pro-American, founded the town of Lamitan which became an American model of civil government and development. Mursalun worked for the material progress of Basilan, and sought ways to fight banditry and piracy in the area. During this time, a famous pirate named Jikiri was attacking the rich Muslim, Chinese, and American traders. He was as much a threat to American rule as the Muslim "insurgents". Although the Yakan were not involved in the growing ties of Jikiri, who was eventually slain by the Americans on 2 July 1909.
There was a resurgence of Moro resistance when Gen. John J. Pershing assumed governorship of the Moro province in 1909. He ordered the complete disarmament of the Muslims through a system of cash incentives, but most refused to sell their weapons. Many Muslims, in fact, decided to resume the fight against the Americans, who were then backed up by Muslim members of the Philippine Scouts (precursor of the Philippine Constabulary). Fierce battles at Bud Dajo and Bud Bagsak in Jolo ensued, forcing the Americans and local counterinsurgency forces to employ the most brutal military tactics against the Muslims. A majority of the victims were women and children, for which Pershing received severe criticism.
Alongside military suppression came a policy of education.
(excerpt from http://litera1no4.tripod.com/yakan_frame)