DNA tests have confirmed the death of Philippines Isis leader known as “Abu Dar”, the last surviving leader of Isis-affiliated Maute Group, after a months-long military operation.

The defence secretary, Delfin Lorenzana, told the Guardian: “It means that the self-proclaimed Isis leader is dead. His group is leaderless in the meantime and also they are scattered after that successful operation by the army.”

The military announced the death of Abu Dar, whose name is Benito Marohombsar, in March after clashes in the town of Tuburan near Marawi, but doubts prompted DNA tests. “Our US counterparts confirmed his death,” Marawi commander Colonel Romeo Brawner told the Guardian.

Abu Dar helped plan the bloody siege of Marawi in 2017 along with the slain Isis emir Isnilon Hapilon and Maute Group leaders Omar and Abdullah Maute, according to a propaganda video shot before the siege. The battle to control the city led to five months of clashes that flattened Marawi’s city centre, which to this day remains practically untouched amid delays to rehabilitation efforts.

Abu Dar had fled to the mountains after the siege but continued to recruit and train fighters. The military launch a huge operation to hunt him down that displaced thousands of residents, sparking humanitarian concerns.

The clashes in Tuburan came weeks after the military overran his camp in the town of Sultan Dumalundong. Abu Dar’s remains were found abandoned beside an improvised litter, showing an attempt to move his body away from the site. A gunshot wound to his back proved fatal.

An image of Philippines Isis leader known as ‘Abu Dar’, or Benito Marohombsar. Photograph: Supplied

Brawner said: “They were trying to run away and maybe because he was dead already, he was left behind. When we found the cadaver, we saw that his face was burnt, probably so we wouldn’t recognise him.”

Abu Dar was believed to be a likely successor of the the Isis emir killed in Marawi, Isnilon Hapilon. The charismatic religious leader linked to influential families was known to be a very effective recruiter. The military claimed he left the battles in Marawi to bring in reinforcements, but was unable to return due to a military blockade.

“Abu Dar was a great speaker, even better than Omar Maute. He was very knowledgeable about the Qur’an. You will really believe him,” a former Maute Group member recruited by Abu Dar said of him. He surrendered to the military last year.

Brawner said Abu Dar’s death had weakened the threat of Isis in Marawi and the nearby towns of Lanao Del Sur province. But the threats from other Isis affiliates remain a concern in other parts of Mindanao, particularly in Sulu and Maguindanao.

Lorenzana said: “We will be monitoring if they attempt to choose another leader and how their remaining force are.”

However, Zachary Abuza, a south-east Asia analyst at the National War College, said attacking its leaders did not address the root cause of insurgencies. “I fundamentally disagree with any counter-terrorism strategy that is based on decapitation. You are not going to kill your enemies out of a long-running insurgency,” Abuza said.