A predominantly Muslim region in the southern Philippines held its first parliamentary elections on Monday, seen as a crucial step in the long quest for self-rule after decades of insurgency and violence.

The Bangsamoro Autonomous Region in Muslim Mindanao was set up under a 2014 peace deal that saw the largest Muslim rebel group give up the goal of a separate Muslim state in the south of the largely Catholic country in exchange for broader autonomy. The group’s 40,000 fighters promised to demobilize and join civilian life. Commission on Elections Chairman Erwin Garcia reported that Cotabato City has been put under the commission’s control, with an administrator to be designated after a shooting incident killed three people and injured 15 others late Sunday. In other incidents in the city, a blast from an improvised bomb injured the person carrying the explosive, and a gun was fired but no one was hurt.

The town of Maluso in Basilan has also been put under the commission’s control after pre-shaded ballots were found in 36 out of 68 precincts. Garcia said he immediately ordered the reprinting of ballots for the affected precincts, where voting would be delayed.

Since the 1970s, about 150,000 combatants and civilians have died in the southern Philippines, while development was stunted in the country’s poorest region. Western and Asian governments feared the tenacious insurgencies could help foster Islamic extremism in Southeast Asia. With bombing attacks and kidnappings, Mindanao used to be a haven for al-Qaida and the Islamic State group before a U.S.-backed Philippine offensive weakened the militants.