Many rebels blame jihadis in their ranks for the West's reluctance to intervene militarily in Syria or give them the advanced weapons they need. There is also growing concern that the dominant role the extremists are playing is discrediting the rebellion.
Yet the jihadis, including members of the Islamic State of Iraq and the Levant, an al-Qaida offshoot, have been some of the most effective forces on the battlefield, fighting alongside the Western-backed Free Syrian Army to capture military facilities, strategic installations and key neighborhoods in cities such as Aleppo and Homs.
But the two sides have turned their guns on each other. Turf wars and retaliatory killings have evolved into ferocious battles in what has effectively become a war within a war in northern and eastern Syria, leaving hundreds dead on both sides.
"The moderates realized that they're losing a lot of territory to the Islamists and jihadi fighters, and so they're more desperate," said Aaron Zelin, a fellow at the Washington Institute for Near East Policy.
The battles for control of Azaz, a town only few kilometers from the Turkish border, represents some of the worst infighting in recent months.
Members of ISIL overran the town Wednesday evening, killing several fighters from the Free Syrian Army rebel umbrella group, before forcing them to pull out.
Amateur video showed dozens of gunmen with heavy machine guns on pickup trucks gathering at the border with Turkey with reinforcements. The Associated Press was able to verify the footage based on interviews and other reporting on the events depicted.
A relatively moderate Islamist group with influence in the region, the al-Tawheed brigade, was mediating Thursday to get the al-Qaida-linked militants to leave Azaz, but fighting was continuing.
The prospect of al-Qaida militants so near the frontier is worrisome for the Turkish government, which closed the nearby border crossing of Bab al-Salameh, according to a Foreign Ministry official speaking on condition of anonymity because he was not authorized to talk to the media.
The Azaz fighting highlights the turmoil in the rebel ranks. Al-Qaida militants and the al-Qaida-affiliated Jabhat al-Nusra have proven remarkably adept on the ground but have increasingly tried to wrest control from more moderate rebels.
Charles Lister, an analyst with HIS Jane's Terrorism and Insurgency Centre in Britain, said al-Qaida-linked fighters make up between 10,000 and 12,000 of the insurgency's estimated 100,000-member force but wield far more influence because of their better discipline and battle experience.
"They (ISIL) capture d from the regime much of the territory that is now under opposition control, and for that reason they will not be excluded from the revolutionary structure even if they have to fight other rebels," said Mustafa Alani, an analyst at the Geneva-based Gulf Research Center.
"They feel that that the FSA has turned on them because the American pressure to deal with extremists," he said.
FSA spokesman Loay al-Mikdad said the rebels were acting in self-defense and questioned the purpose of the ISIL storming an area that had been among the first to be "liberated" in Syria.
"They said they came to defend the Syrian people. Now they have turned their guns away from fighting the regime to fighting the Syrian people," he said by telephone from Turkey.
Kurdish militiamen have also been fighting members of the ISIL and the Nusra Front in predominantly oil-rich, Kurdish areas of northeastern Syria. Dozens have died.
The infighting weakens both sides and bolsters Assad, whose troops have been on the offensive, gaining ground against rebels on multiple fronts.
Assad told Fox News Channel the balance of opposition forces has shifted in the more than two-year conflict, and he alleged that 80 percent to 90 percent were members of al-Qaida or its affiliates.
"At the very beginning, the jihadists were the minority. At the end of 2012 and during this year, they became the majority with the flow of tens of thousands from additional countries," he said.
Residents of rebel-held areas are also turning against extremists for their brutal tactics and for trying to impose Islamic law. There have been numerous demonstrations against the ISIL in opposition-held territory in the north.
Locals say the jihadis are forcing people to close their shops for Muslim prayers and banning the sale of cigarettes.
Ahmad Barbour, an activist in the town of Ariha in the northwestern province of Idlib, said it has gotten to the point where they consider those who carry the revolution flags infidels. Most of them are foreigners flush with cash, he said.
"Everyone hates them except for those who are benefiting financially," he said via Skype.
Also Thursday, a bus struck a roadside bomb in the village of Jbourin in the central province of Homs, killing 19 people and wounded four, said a local official from the governor's office, speaking on condition of anonymity because he was not authorized to talk to the media.
The village is predominantly Alawite an offshoot of Shiite Islam and a minority sect of which Assad is a member but it also has Christians and Sunni Muslims.
The civil war, which has left more than 100,000 dead, has taken increasingly sectarian overtones. Most of the rebels trying to overthrow Assad belong to the majority Sunni sect.
Syrian Deputy Prime Minister Qadri Jamil said in an interview with the Guardian published late Thursday on its website that neither side in Syria was strong enough to win the conflict. Jamil said the government will call for a cease-fire at a planned peace conference in Geneva, though dates for the talks have not been set and the main Syrian opposition group says it won't take part if the military has the upper hand on the ground.