The rival groups are already plotting for a post-Assad Syria, jostling for power to improve their chances at calling the shots in the future.
Countless armed groups have emerged since last year, loosely coming together to form the Free Syrian Army as the uprising gradually transformed from a peaceful uprising into an armed rebellion in the face of the regime crackdown.
But the FSA lacks both a clear structure and a strong central leadership.
Reflecting popular concern over a lack of coordination among rebel groups, anti-regime demonstrators took to the streets on Friday under the slogan: "If our Free Army is united, victory is assured."
The FSA's command in Syria comprises 10 military councils headed by military defectors, and which brings together thousands of fighters – most of them civilians who have taken up arms and joined the insurgency.
But many groups – including Islamist battalions – claim a certain autonomy from the FSA's leadership, even if they consider themselves part of it.
"Our leadership is independent," said the Muslim Brotherhood-funded Tawhid Brigade's Abdel Qader al-Saleh, chief of operations in the northern hub of Aleppo that has witnessed some of the fiercest fighting.
"When we decided to join the battle for Aleppo, we did not consult with the military council," Saleh told AFP. "Why should we? We have the biggest number of fighters in Aleppo and its surroundings."
Saleh criticized the military councils' leadership, saying he would coordinate with fighters in the field, "not with people sitting behind their desks." He also described meetings with the military councils as mere "coffee breaks."
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Muslim Brotherhood making its move
"Islamist brigades get most of their funding from Qatar and Turkey," rebel commander Abu Mussab told AFP. The military councils, meanwhile, receive non-lethal support from Saudi Arabia, the United States and the European Union.
"Al-Qaeda finances the jihadis, the Muslim Brotherhood fund the moderates, and the rich Saudis indiscriminately finance both," he added.
Experts say jihadis constitute a small minority of fighters in the insurgency.
Many seemingly Salafi fighters only grow long beards and wear Islamic garb in order to benefit from funding from conservative powerhouse Saudi Arabia, a Britain-based expert on Syria told AFP on condition of anonymity.
But it is the Muslim Brotherhood, which has been exiled from Syria since the 1980s, which provides the majority of the funding, assistance and weapons, activists and rebels say.
Their goal, it seems, is to monopolize aid in a bid to carve out the lion's share of power, when and if Assad goes.
The West's reluctance to arm the rebels has forced them to radicalize and appeal to Salafi groups, which provide both funding and know-how, the FSA's Joint Command spokesman Kassem Saadeddine told AFP via Skype.
The United States and European countries have frequently warned that Syria's formidable military arsenal – which includes chemical weapons – may eventually fall into the hands of extremists.
"The rebellion will only become more Islamic and may even get out of hand should the situation get out of (FSA) control," said Saadeddine.
No doubt, divisions on the ground are a worrying sign of things to come in a post-Assad Syria. Frequently, the rebels have lost battles precisely because of their lack of coordination.
"One rebel group's surprise withdrawal from a main road in the once rebel-held Bab Sbaa district of (the central city of) Homs a month ago – without consulting the rest, meant the whole of the district could be reclaimed by the regime," an activist who identified himself as Rami al-Homsi told AFP.
But Saadeddine was keen to emphasize that now is not the time for settling scores.
"We all share one goal: to bring down the regime," he said.
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