The history of the Subanon is obscure until the 1600's, when they are mentioned in the writings of Spanish Jesuit missionaries. Prior to the twentieth century, their only contact with the outside world was with Muslim merchants who lived along the coast of the peninsula. The Muslims exploited them economically, setting the pattern for Subanon relations to this day.
Since World War II, Christian and Muslim ethnic groups of the Philippines have often clashed. The Subanon, who are polytheists (believe in many gods), have been caught in the crossfire, victimized by one side, then the other.