Two top Philippine commanders of an armed alliance that has declared loyalty to the Islamic State of Iraq and the Levant (ISIL, also known as ISIS) group, have been killed, according to authorities, in a major blow to an ongoing armed rebellion in the country's south.

Isnilon Hapilon, the top commander of the Abu Sayyaf Group and Omarkhayam Maute of the Maute Group, as well as seven of their fighters, were killed on Monday, after military forces launched a major operation in the besieged city of Marawi, General Eduardo Ano, the top military commander, said in a press conference.

Ano said information provided by a female hostage, who escaped recently, led the government troops to the location of the armed fighters.

He added that the two commanders had never intended to give up arms, quoting them as telling the escaped hostage, "We will not surrender. We will die fighting".

Hapilon had a $5m bounty on his head issued by the US government. The government of the Philippines has also offered $200,000 for his capture, and a separate $100,000 for Omarkhayam.

Ano said dozens of fighters, including foreign nationals, remain holed up in one section of Marawi, and they are believed to be still holding hostages.

But with the deaths of Hapilon and Maute, "it is just a matter of time" before the siege will be over, Ano said, referring to the five-month battle that has left over 1,000 people dead, about 600,000 others displaced, and a historic city destroyed to the ground.

The siege of Marawi started when military and police tried to serve an arrest warrant against Hapilon in May. Instead of giving up their arms, Hapilon formed an alliance with the Maute Group and launched a bloody rampage across the university town by the picturesque Lake Lanao. That prompted President Rodrigo Duterte to declare martial law in Mindanao.

Hapilon's notoriety has spanned almost two decades as one of Abu Sayyaf's top commanders in the islands of Basilan and Sulu, where the group has been involved in kidnappings and beheadings of hostages including several foreigners.

Multiple military operations have been conducted against the group, which previously aligned itself with al-Qaeda. But Hapilon managed to evade the military dragnet several times.

Hapilon then switched his allegiance to ISIL, becoming its self-appointed Southeast Asian commander.

Earlier this year, he and his men moved to the province of Lanao del Sur to join forces with the ISIL-inspired Maute Group. The group was led by the brothers Omarkhayam and Abdullah. Abdullah and two other Maute brothers were reported killed by the military in September.

'Historical injustices'

Shidik Abantas, legal officer at Mindanao State University in Marawi, said the military operation on Monday was "very significant in a sense that the end of the siege is almost here".

"As to whether it will bring peace, it is complicated," Abantas told Al Jazeera.

"The rise of extremism in Mindanao, especially in our locality, is not really caused by the ISIS in the Middle East. It is mostly caused by the historical injustices that continue to this day."

As a local, he said he feels "depressed and annoyed" at the siege and destruction of Marawi, which he said were both preventable.

"The instant use of aerial bombings and the absolute abandonment of all forms of negotiation has led to the destruction of Marawi," he said.

"The destruction of the city has brought about mistrust between the locals and the government."

He also said that the "insistence of the government" to link locals to the armed fighters despite "zero or unsubstantial evidence" worsened the conflict.

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Root of 'extremism'

Jay Batongbacal, lawyer and Southeast Asian Studies expert at the University of the Philippines, said Monday's operation was a "major blow" to Abu Sayyaf, setting it back "for a few years".

"But it does not mean that the Abu Sayyaf has been completely eliminated," he said, adding that the group has shown "resilience and adaptability" since it emerged in the 1990s.

"Experience has shown that it tends to lie low and then re-emerge as a threat after a while, with new leadership," Batongbacal told Al Jazeera.

"For as long as the social and economic conditions in Mindanao have not improved, the Abu Sayyaf will find fertile ground for a comeback."

Meanwhile, a retired senior military commander warned that a new generation of fighters could emerge from the Marawi conflict.

"The fighting and destruction in Marawi could inspire a generation of young Muslims to consider, or even adopt the fundamentalist ideology of ISIL," the retired officer, who asked not to be named to freely discuss the long-running rebellion, told Al Jazeera.

He said the extent of destruction of Marawi could "exacerbate" the situation.

"The Marawi conflict proved to be a serious challenge to the government and its security apparatus and has grave implications to the Philippines' war against terrorism," he said.

"The fact that the rebellion has practically held the nation and the military hostage for several months is a grave development.

"The terrorist group in Marawi was not a ragtag one, but a formidable force, well-organised, well-equipped, and highly motivated.

"The death of the duo and the end of Marawi hostilities may signal a temporary weakening of the movement. But the threat continues and may even evolve into a more serious and radicalised one."

'Beginning of bigger battle'

For Alia Fatma Macarambon, a student and resident of Marawi, the conflict is personal.

"This war broke my heart, every picture, every news regarding the war makes me cry, because it is not the Marawi that I know," she told Al Jazeera.

"It saddens me that there are so many innocent persons killed. I have close relatives and friends who have no home to go back to."

Ace Guro, an ethnic Maranao whose family hails from Marawi, said that while the latest development signals the war may be over soon, it is only "the beginning of a bigger battle" for her people.

"To be honest, some of us have considered not going back because the city is no longer the home it used to be. But those who do not have the privilege to leave will stay," she said.

Guro said the government should have a clear plan for rehabilitation that would give "incentives" for locals to work with the government.

"We need to build that kind of trust between each other to make things work. We want to make sure that what happened in Marawi will not go down in history as a mere crisis but as a success story of how we defeated terrorism despite being accused of such.

"Aside from the buildings that need to be fixed again, I think it's important to heal the wounds that we don't see, the spirit of the Maranaos that have been shaken by the crisis."