Islam touched the shores of the Philippine Islands way before American and Spanish colonizers did (AI-Attas:1969). The Islamization of the Philippine Archipelago was part of the spread of the religion in the Southeast Asian region. Islam is not merely a religion, as noted by many Muslim scholars but is as well a way of life (Doi: 1984). Thus, when Islam spread throughout the country, it also introduced a system of government and a sophisticated culture.

Islam introduced a highly developed political structure, the Sultanate. The traditional Muslim social structure in the Philippines was headed by a sultan who assumed both religious and secular authority. The Datu assumed communal leadership, providing aid and arbitration through agama courts under his leadership. The wealth amassed by the conquests of the Datu is provided to his subjects for aid, employment, and protection when needed. Interestingly, the Datu is not determined by his wealth but by the number of his followers. Further, the holy Qur'an, the source of both secular and religious precepts and laws of Muslims, provides a sense of oneness and fraternal bond between Muslims as an Ummah or Islamic Nation (21:92). Islam changed the country's once fragmented nature into a single nation (Bangsa Tungga).

Thus, when the colonizers came and threatened the growth of their government, much resistance was felt, especially in Southern Philippines where Muslim communities were most concentrated. The Spanish assimilation only succeeded in creating rifts between the Christianized Filipinos under Spanish rule and the Muslim communities that refused subjugation (Majul: 1973). It was the same during the American Regime, if not worse, wherein they employed a process of extermination through military troops when the Muslims refused subjugation and resisted the exploitation of resources within the Mindanao region (Tan: 1977). The Americans realized then that the process was futile and assumed a strategy for winning the Muslims, through the establishment of a special bureau for their affairs and concerns (Gowing: 1983).

However, through these years, from the American initiative to integrate Muslim communities with the majority of the Filipinos, divisiveness in culture and religion has spread and grown into social unrest and conflict situations. The Muslims remained isolated from the developments provided by the government in the northern regions of the Philippines, separatist movements grew, and resentments between Christians and Muslims developed (Fernando: 1979, Rahman: 1954).

The Philippine government in several instances tried to address the issues of the country regarding Muslim separatist movements through policies and the creation of several offices. The Tripoli Agreement was developed to grant political autonomy for two Muslim regions, and recognition of their "cultural values, traditions, and customary and Islamic laws, in the formulation of State policies."

Several agreements have been signed since, and still much has yet to
be resolved.