The fall of the town of Atma, a crossing point for weapons and for Syrian rebels, signals disarray among some of the rebel groups, which are ceding ground to hardline Islamist units.
Some of these groups are now playing a lesser role on the battlefield in the war against President Bashar al-Assad's forces, opposition sources said.
The rise of al Qaeda in Syria has helped change the international diplomatic calculus and tempered Western calls for Assad's removal from power.
Europe and the United States have baulked at military intervention in the conflict and are negotiating with Russia, Assad's main international backer, to hold peace talks.
Activists said fighters of the al Qaeda affiliate - Islamic State in Iraq and the Levant, or ISIL - had stormed the headquarters of Suqur al-Islam, a moderate Islamist unit that controlled Atma, and set up roadblocks within the last 48 hours.
They detained Mustafa Waddah, the head of Suqur al-Islam, along with two dozen of his men.
A brief firefight took place at the headquarters and also near a Turkish security post in the town of Bükülmez, which overlooks Atma and its hilly terrain, the sources said.
With its proximity to Turkey, Atma has been largely spared shelling and air raids by Assad's forces. But thousands of people who fled bombings elsewhere in the country had taken refuge in the town and surrounding area.
"The ISIL deployed anti-aircraft guns at the main roundabout and took Atma quietly," said one of the activists, who did not want to be named.
"The Turks have not stopped supplies from crossing into the town and movement across the border fence is normal."
He said Waddah's whereabouts were not known, but he may have been taken to the town of Dana, an ISIL stronghold where the group had set up a religious court.
Suqur al-Islam is a unit of the Free Syrian Army General Staff, headed by General Selim Idriss, the main opposition military figure, who is based in Turkey. But Suqur al-Islam and the General Staff have fallen out over sharing the weapons crossing through Atma, the activists said.
In the last few days, fighting erupted between Sukur al-Islam and other Free Syrian Army members after Sukur al-Islam seized seven trucks loaded with weapons sent by the General Staff that crossed through Atma.
"Suqur al-Islam were exhausted after the fighting with the General Command and the ISIL walked easily into their headquarters," said Abdallah al-Sheikh, an activist in Atma.
"Basically there was collusion between the General Staff and the ISIL."
Officials of the Free Syrian Army General Staff were not immediately available for comment.
Free Syrian Army units, including Sukur al-Islam and the ISIL had cooperated in the region before, mainly to fight Kurdish militia linked to the Kurdistan Workers Party who had encroached on Atma, the activists said.
However, the two sides have also fought against each other, underscoring the complex relationships among Assad's foes.
In August the ISIL took control of the northern border town of Azaz, expelling another Free Syrian Army unit and prompting Turkey to close a nearby border crossing.
The Syrian uprising against four decades of Assad family rule started in 2011 and erupted into a full-scale civil war after Assad's forces shot demonstrators and deployed tanks to crush the protest movement. More than 100,000 people have been killed and millions have been displaced.