Ameril Umbra Kato formed the Bangsamoro Islamic Freedom Fighters (BIFF) and led the rampage after splitting from the nation's main rebel group, the Moro Islamic Liberation Front (MILF), in anger over a planned peace deal.
The rebel leader, believed to be in his late 60s, suffered a fatal stroke early yesterday, leaving behind an armed force of about 150 guerrillas, military spokesman Colonel Harold Cabunoc told AFP.
"We're 99.9 per cent sure he's dead. We just don't have the body," he said, citing three "assets" close to Umbra Kato's organisation.
Mama said Esmael Abubakar, whom he described as a "Middle East-trained ulama" or Muslim scholar, was elected to replace Umbra Kato.
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Umbra Kato's death followed a five-week military campaign that ended last month to flush out foreign and Filipino militants wanted by the United States who had sought refuge in BIFF camps on the main southern island of Mindanao.
Though relatively small, Umbra Kato's group was blamed for attacking at least nine Mindanao towns in 2008, with the assaults claiming about 400 lives and forcing 600,000 people to flee their homes.
Captain Joan Petinglay, a military spokeswoman in the area, told AFP that Umbra Kato's death was not expected to impact the BIFF greatly.
"The death affected their morale for sure. But in terms of the conduct of their operations the effect is minimal," Petinglay said, adding Umbra Kato has been known to be ill for some time.
Filipino security analyst Rodolfo Mendoza and Cabunoc said the group's announced choice for a new leader came as a surprise, and may indicate its desire to be seen as more moderate.
He said the Kato son "has been very close to the foreign jihadists".
Cabunoc also said it was Karialan who pledged the BIFF's allegiance to Islamic State fighters."
"Our reading (of the group's surprise choice of new leader) is that they want to avoid being tagged as terrorists," he added.