Editor's note: Peter Bergen is CNN's national security analyst, a director at the New America Foundation and the author of "Manhunt: The Ten-Year Search for bin Laden -- From 9/11 to Abbottabad."
(CNN) -- When even al Qaeda publicly rejects you because you are too brutal, it's likely a reasonable indicator that you are.
A long simmering dispute between "al Qaeda Central," headed by Ayman al-Zawahiri, and the most brutal al Qaeda affiliate in Syria, generally known as the Islamic State of Iraq and Syria, surfaced publicly on Monday.
On jihadist websites, al Qaeda's central leadership posted a notice saying ISIS "is not a branch of the al Qaeda group."
It is the first time in its quarter century history that al Qaeda has officially rejected one of its affiliates.
Why did this happen? ISIS and another al Qaeda affiliate known as the Nusra Front have been fighting each other in Syria for several weeks now.
This open warfare caps a dispute between ISIS and Nusra about who is boss in Syria that has been brewing since ISIS released a statement in April announcing its official merger with Nusra.
A leader of Nusra rejected the merger, and in June, al-Zawahiri annulled the merger. ISIS, in turn, rejected al-Zawahiri's annulment of the merger. (This is a fine example of what Freud usefully termed "the narcissism of minor differences.")
Al-Zawahiri is clearly fed up with ISIS's open rejection of his overall leadership of the al Qaeda network. Moreover, he is likely quite concerned about how ISIS is alienating ordinary Syrians by a brutal campaign that has involved the public beheading of opponents and the imposition of Taliban-style rule on the population, including the banning of smoking, music and unveiled women in public.
Al Qaeda's leader has seen this movie before -- in western Iraq in 2006, when al Qaeda in Iraq (the parent organization of ISIS) imposed a brutal Taliban-like rule on the population that caused the Sunni tribes in western Iraq to rebel against al Qaeda in an uprising known as "the Sunni Awakening."
The Sunni Awakening, with a heavy assist from the U.S. military, led to al Qaeda losing control of much of western Iraq by 2008.
Nusra seems to have learned from the mistakes of al Qaeda in Iraq and is not imposing Taliban-style rule in the areas of Syria that it controls and is instead operating in a Hezbollah-like manner, providing social services. The group, for instance, provides bread and electricity in the eastern Syrian city of Ash Shaddadi, where it also controls the city's wheat silos and oil wells.
Nursa also is engaging in the kind of alliance-building that al Qaeda affiliates generally have not been able to pull off because they regard compromise as a deviation from their God-given beliefs. Nusra has, for instance, allied with more moderate elements of the Syrian opposition to fight against ISIS during the past several weeks.
Nusra, in fact, represents what al Qaeda's core leadership wants in one of its affiliates: A group that doesn't tarnish the al Qaeda brand by using brutal tactics against fellow Muslims.
This has been a core concern for al Qaeda for the past decade. Al-Zawahiri sent a letter to al Qaeda in Iraq in the summer of 2005 admonishing the group against its campaign of killing Shia civilians.
Similarly, Osama bin Laden wrote a private letter to the al Qaeda-aligned Somali terrorist group, Al-Shabaab, in 2010 telling the organization to stop attacking in the central market of the Somali capital, Mogadishu, because such attacks were killing Muslim civilians.
Also in 2010, al Qaeda leaders wrote a private letter to the leader of the Pakistan Taliban telling him forcefully to suspend his group's campaign of attacks against mosques and markets, which was killing hundreds of Pakistani civilians.
The difference now is that al Qaeda has gone public with its displeasure with ISIS and is also officially cutting the group off.
Despite the bitter differences between the two al Qaeda-aligned groups in Syria, senior U.S. counterterrorism officials tell me they are "All Syria. All the time."
That is because al Qaeda affiliated groups in Syria and neighboring Iraq now control more territory in the Arab world than at any time in their history; a swath of land that runs from northwestern Syria some 400 miles to the east into western Iraq.
On Tuesday, CIA Director John Brennan testified before the House Intelligence Committee: "There are camps inside of both Iraq and Syria that are used by al Qaeda to develop capabilities that are applicable, both in the theater, as well as beyond." Brennan asserted that these camps represent a real threat to the United States.
Adding to their concerns, U.S. counterterrorism officials tell me that more Americans have traveled to fight in Syria than was previously understood. They believe some 70 Americans have fought there over the past three years. Previous estimates suggested only a handful of Americans had done so.
U.S. counterterrorism officials are rightly concerned that Americans who have fought in Syria will return to the States radicalized and perhaps even to plan to carry out terrorist attacks.
That said, it isn't clear how many of the 70 Americans who are estimated to have fought in Syria have done so alongside the al Qaeda-aligned groups or with other more moderate rebel groups who are fighting the Bashar al-Assad regime with some degree of American support.
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