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The move is seen as an attempt by Al-Qaeda to reassert its authority over fragmented fighters involved in Syria's three-year-old war, which remains largely deadlocked, with the country split into areas controlled by the government of President Bashar al-Assad and the opposition.
The statement, which was attributed to the Al-Qaeda "General Command," said that ISIL "is not a branch of the Al-Qaeda group."
Al-Qaeda's leader Ayman al-Zawahri last May ordered ISIL to operate independently from the Nusra Front, another Al-Qaeda-linked group. However, ISIL leader Abu Bakr al-Baghdadi rejected al-Zawahri's orders and unsuccessfully sought to merge the two branches.
In Monday's statement, Al-Qaeda said it "did not approve of the creation of, nor did it control" the ISIL, and therefore has "no organizational ties with it."
"We distance ourselves from the sedition taking place among the mujahedeen factions (in Syria) and of the forbidden blood shed by any faction," the statement said of the fighting among ISIL and opposition groups.
ISIL follows Al-Qaeda's hardline ideology and, until now, the two groups were seen as linked.
"ISIL has become completely isolated in Syria," Joshua Landis, director of the Center for Middle East Studies at the University of Oklahoma and a Syria expert, told Al Jazeera. "All the other militias will be attacking ISIS."
"Nusra (the Nusra Front) will be the big gainer, as it is recruiting ISIL defectors," Landis said.
He added that the Islamic Front, an alliance of six major Islamist rebel factions in Syria, has been warning Nusra against mass recruitment of ISIL defectors for "fear that Nusra will begin attacking others."
Ultimately, Landis said, "the Islamist militias are in disarray and the infighting is demoralizing fighters and funders alike."
Charles Lister, visiting fellow at Brookings Doha Center, also told Reuters that the Al-Qaeda statement "represents an attempt by Al-Qaeda to definitively reassert some level of authority over the jihad in Syria" following a month of ISIL disobedience.
"This represents a strong and forthright move by (Al-Qaeda) and will undoubtedly serve to further consolidate Jabhat al-Nusra's (the Nusra Front) role as Al-Qaeda's official presence in Syria," Lister said.
ISIL has fought battles with other hardline Sunni insurgents and secular rebel groups, often triggered by disputes over authority and territory. Several opposition groups announced a campaign last month against ISIL.
Rebel-on-rebel violence in Syria has killed at least 2,300 this year alone, according to the Syrian Observatory for Human Rights, an opposition monitoring group.
The infighting has added another bloody dimension to the Syrian crisis, which erupted in March 2011 as an uprising against Assad's rule but later evolved into an armed insurgency and civil war.
Hardline rebels, including Nusra, have come to dominate the largely Sunni Muslim insurgency against Assad, who is supported by his minority Alawite sect — an offshoot of Shia Islam — as well as Shia fighters from Hezbollah.