The Moro Rebellion (1901-1913) occurred after the conclusion of the Philippine-American War and involved sporadic confrontations between the Muslim Filipinos living in the southern part of the Philippines and the American soldiers there to oversee the transition from Spanish rule to U.S. oversight.
The Moro peoples had assumed that once the Philippines were liberated from the Spanish, they would be self-governing. They resisted the American takeover of the Philippines in 1899, centering their fighting in the island of Mindanao and the Sulu Archipelago, and loosely organized around the Sultan of Sulu.
On July 4, 1902, President Roosevelt declared victory in the Philippine-American War, but the peace treaty did not apply to the Moro peoples in the South who continued to battle against U.S. forces. Just under a year later, the Roosevelt administration created the Moro Province and shortly after installed Leonard Wood as provincial military governor. Wood was unable to pacify the Muslim Filipinos, but he mandated an end to slavery. Tasker H. Bliss replaced Wood, serving as military governor from 1903-1909, a time of relative peace. John J. Pershing brought an end to the Moro Rebellion of the early twentieth century when he served as the last military governor from 1909-1913. Pershing brought about the disarmament of the Filipinos in the Moro Province. Frank Carpenter became the first civilian governor in 1913.
President Roosevelt made plain his belief that because the Filipinos could not govern themselves and would profit from American occupation, it was the duty of the United States to maintain the Philippines as a protectorate. (See for example, “The Strenuous Life,” speech before the Hamilton Club, April 10, 1898, and “Expansion and Peace,” The Independent, December 21, 1899.) The Philippines ceased being a protectorate of the U.S. on July 4, 1946.