Competition between the United Courts Council and courts backed by the Nusra Front exploded this month. On Tuesday, the council accused Nusra Front fighters of raiding one of its courthouses in Aleppo.
"Jabhat Al-Nusra stormed the Second Circuit United Judicial Council and seized the building of the Council and attacked scholars and judges who were there and they beat them and insulted them and then they kidnapped them to Jabhat al-Nusra's headquarters," said the council in a written statement also signed by a group calling itself the Free Aleppo Lawyers.
It is not the first time tensions have flared between the Nusra Front and other revolutionaries.
One of Aleppo's most famous anti-government activists, a man known as Abu Maryam, told CNN he was briefly detained and flogged by Islamist fighters last week.
After his release, Abu Maryam posted a photo on Facebook of his bruised back.
"They accused me of protesting against the caliphate," Abu Maryam said in a brief interview with CNN.
Asked whether he thought the Nusra Front was taking over Syria's uprising, Abu Maryam said, "Yes, of course, that's true, but it's all because of the mistakes of the Free Syrian Army."
Nearly two years into the uprising, the rebel Free Syrian Army continues to be dogged by accusations of corruption.
In recent weeks, activists have mounted an online campaign accusing Ahmed Afash, a prominent commander based in Aleppo, of banditry and kidnapping. Afash has denied the charges.
But last week, a detachment of Afash's fighters raided the offices of the Aleppo Media Center. They briefly detained several Syrian journalists who had published reports that Afash's brigade had killed an innocent civilian.
Meanwhile, Islamist groups like the Nusra Front have been applauded for distributing food and fuel to hungry, freezing Syrians.
The Nusra Front also launched a cheap public service in rebel-controlled parts of Aleppo.
"Not only do they do the fighting, but they also perform a lot of civil duties such as cleaning roads, manning bakeries, installing and repairing city infrastructure like electricity," said the activist from Idlib province, who asked not to be named. "Some of the Nusra Front members are now playing even the role of street cleaners because of garbage in the city that has increased the rat population."
Even Syrians who criticize the Nusra Front concede the Islamists have offered hope to some members of a society traumatized by a brutal conflict that has claimed more than 70,000 lives and left millions of people homeless.
As Islamists within the uprising continue to attract support, leaders of the Free Syrian Army have been left fuming, blaming a lack of Western engagement for the ideological shift in the uprising.
"We see the Islamist factions gaining more ground, recruiting some of our own people," said Louai Miqdad, a spokesman for the Free Syrian Army.
"The world is handing Syria over to the unknown, to the radicals, to the Islamists."