And while senior leaders of Al-Qaeda were all but above question under revered founder Osama bin Laden, the conflict has gone so far that even his replacement Ayman al-Zawahiri has come in for fierce criticism on jihadist forums online.
Powerful rebel groups in Syria, including Al-Qaeda's designated local affiliate Al-Nusra Front, have been locked in fierce fighting with jihadist group the Islamic State of Iraq and the Levant (ISIL), with thousands of people killed since January.
But allegations of brutal abuses against civilians and rival fighters sparked a backlash and even accusations that they served Assad's interests.
In a sign of how sharp the divisions have become, ISIL spokesman Abu Mohammed al-Adnani has accused Al-Qaeda leaders of betraying the jihadist cause.
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"Al-Qaeda today is no longer a base of jihad (holy war)," Adnani said in a statement posted on jihadist forums, playing off the militant group's name, which means "the base" in Arabic.
"Its leadership has become a hammer to break the project of the Islamic State," Adnani said, adding that "the leaders of Al-Qaeda have deviated from the correct path".
Online, the clash among jihadists has seen criticism of Zawahiri from around the Islamic world, though others have defended the Al-Qaeda chief.
"Zawahiri has fallen... We will not listen to him any more. To the dustbin of history, oh Al-Qaeda," tweeted ISIL supporter Munassar al-Mumineen.
Ahmed, another Twitter user, attacked Zawahiri as "old" and called him "the Prince of the Khawarij" - those who have left the proper path of jihad.
Charles Lister, a visiting fellow at the Brookings Doha Centre, said the dispute is ultimately over leadership of the jihadist movement.
"This continuing battle for influence between Al-Nusra and ISIL has the potential to cause shock waves across the international jihadist community.
"The conflict in Syria has provided an enormous opportunity for jihadist groups, and with such a significant opportunity comes the possibility of divisions," he added.