The Muslim south is not a minority that arrived; it is the part of the archipelago Spain failed to conquer. Sultanates at Sulu and Maguindanao predated Spanish arrival and survived it, and the Spanish word for Philippine Muslims, Moro, was carried over from the Iberian Reconquista and has been reclaimed as a national name. American administration and then Philippine government resettlement policy moved large numbers of Christian settlers from Luzon and the Visayas into Mindanao through the twentieth century, turning Muslims into a minority in much of their own region and creating the land disputes that underlie the conflict.
Armed struggle began in earnest after the Jabidah massacre of 1968, with the Moro National Liberation Front and later the Moro Islamic Liberation Front, and continued for more than four decades at a cost of well over a hundred thousand lives. A 2008 agreement was struck down by the Supreme Court, and the 2015 clash at Mamasapano that killed forty four police commandos nearly destroyed the process.
The Bangsamoro Organic Law was eventually ratified by plebiscite in 2019, creating an autonomous region with its own parliament and a Sharia jurisdiction over Muslim personal status. Its durability is the open question, complicated by the 2017 siege of Marawi by fighters pledged to the Islamic State, which destroyed the largest Muslim city in the country.