The two leaders were named as Isnilon Hapilon, who was declared terror group’s emir for Southeast Asia, and Omar Maute, a leader of a local militant group that had pledged allegiance to ISIS.
Their bodies have been recovered, the Defense Department said in a statement. Seventeen civilian hostages were also rescued, it added.
The FBI had offered a reward of up to $5 million for information leading directly to Hapilon’s apprehension or conviction for a litany of alleged crimes, including hostage taking, murder, and terrorist activities.
The battle for Marawi began on May 23, when the military launched an operation targeting Hapilon on the island of Mindanao, where Marawi is located.
Hapilon was thought to have issued an emergency call for reinforcements from members of the Maute group, which was headed by Omar and his brother Abdullah.
Abdullah was rumored to have been killed in early September, but the military has yet to confirm his death. Omar’s death had been reported multiple times in the past, though never confirmed.
After Hapilon called for backup, militants poured into the city by the hundreds, setting fire to buildings, taking hostages and entering into running street-battles with government forces.
The violence forced over 350,000 residents to flee the city and the surrounding areas, and saw President Rodrigo Duterte declare martial law across the island shortly after.
The Philippines Congress granted Duterte’s request in July to extend the emergency measure until the end of the year, despite questions over the move’s constitutionality.
The evasive leader
Hapilon, a skinny, baby-faced 51-year-old with a tufty goatee beard, had been dodging Philippines authorities for over a decade, since he emerged as a ruthless and deadly commander of the Abu Sayyaf militant group in the early 2000s.
Abu Sayyaf is a violent extremist group with a history of kidnappings-for-ransom and bombings that split from the separatist movement the Moro National Liberation Front in 1991. The group is fragmented and there is no unified command.
The group is thought to have several hundred members — and maintains strong ties to other local militant groups, according to the Jakarta-based Institute for Policy Analysis of Conflict (IPAC). It operates in the semi-lawless tri-border area between the Philippines, Malaysia and Indonesia, which has long been a haven for smugglers, pirates and other criminals.
Last year, Hapilon — who headed a major faction of Abu Sayyaf — was designated by ISIS as the terrorist organization’s emir for Southeast Asia and commander of the so-called Brigade of the Migrant based on the southern island of Mindanao and made up of fighters from Malaysia, Indonesia and the Philippines.
Though a various disparate militants have operated in the region for years, analysts told CNN that Hapilon’s elevation to ISIS emir led to greater unity between the various organizations in the area.
Despite the hefty bounty on his head — and pursuit by US and Philippines special forces — Hapilon managed to avoid capture for 16 years.
During that period, the tactics deployed by Abu Sayyaf grew more extreme and more deadly.
In 2004, the group bombed a passenger ferry in Manila Bay, killing 116 people, while in 2014, Abu Sayyaf militants attacked civilians celebrating the end of Ramadan, in Talipao, in Sulu province in the far south west of the country, killing at least 21, according to the US State Department.