Islam is one of the oldest organized religions to be established in the Philippines. The first indication of the presence of Islam in Manila dates to about 1175 A.D., as evidenced by a graveyard at Santa Ana Church in Manila, where human remains oriented toward Mecca were found. Islam came to Sulu in the middle of the 13th century. It is said that had the Spaniards not introduced Christianity in central and northern Philippines in the 16th century, the whole country would have been practicing Islam.

The Sulu Sultanate was established in 1450 among the Tausug and Sama by Hashim Abubakar, indicating the Islamization of an indigenous institution. In 1475 the Malaysian Sharif Kabungsuan arrived at the mouth of Pulangi River accompanied by a small force of Sama warriors. This event ushered in the Maguindanao’s conversion to Islam, which spread slowly through the Philippines beginning in the island chains of Tawi-Tawi. But even before these stipulated dates of arrival in Sulu and Maguindanao, Islam must have already filtered in earlier, as far north as Manila. Kabungsuan married the daughter of a Maguindanao chief and later became their leader. Through the use of swords and bows and arrows introduced by Kabungsuan, the Maguindanao conquered the adjoining ethnic groups. The Maguindanao sultanate developed, dominating a network of local autonomous datus bound together by kinship and marriage. Another Islam-influenced sultanate in the south is that of the Maranao in Lanao del Sur.

The influence of Islam spread eastward, along the southern coastline, reaching Davao Gulf by the 19th century. By 1648, Sultan Kudarat ruled the entire area they occupied. They had extensive trade with Southeast Asians and Europeans. Traders occupied coastal Maguindanao, while producers settled in the interior. They traded rice with the Dutch East Indies Company, principally for clothing. Rice was produced in the Cotabato basin with labor coming from bondsmen and slaves. The Spaniards later tried to subdue the Maguindanao, but it was only in 1861 that the Maguindanao sultanate finally submitted.