In fact, human fossil remains found in Palawan suggest the country's "modern" history goes back 50,000 years when humans first migrated across land bridges formed to mainland Asia and Borneo during the Ice Age. The islands were eventually inhabited by different groups, the first of which was the Aeta or Negritos , a tribe that arrived around 25,000 years ago from the Asian continent. Many historians believe the Negritos are the true aboriginal inhabitants of the Philippines.

Archeological evidence shows a rich pre-colonial culture that included skills in weaving, ship-building, mining and goldsmithing. Contact with Asian neighbours dates back to at least 500BC in the form of trade with the powerful Hindu empires in Java and Sumatra. Trade ties with China were extensive by the tenth century, while contact with Arab traders reached its peak in the twelfth century. In 1380, the Arab scholar Makdam arrived in the Sulu Islands, and in 1475, the Muslim leader Sharif Mohammed Kabungsuwan, from Johore, married a native princess and declared himself the first sultan of Mindanao. By the time the Spaniards arrived, Islam was well established in Mindanao and had started to influence groups as far north as Luzon.