A new front is opening in the Syrian civil war that looks set to pit rebel against rebel, as confrontations between Western-backed groups and Islamic fundamentalist fighters threaten to spiral out of control.

The assassination of a leading commander of the Free Syrian Army by fighters allied with al-Qa’ida will further divide the rebels in Syria at a time a moment when they are struggling to deal with government forces offensives against opposition strongholds.

Kamal Hamami was killed on Thursday along with his brother at a checkpoint near Latakia in north-west Syria. The assassination was reportedly carried out by the Islamic State of Iraq and the Levant, which has long been conducting a guerrilla war against the Iraqi government and fighting under the banner of the al-Nusra Front in Syria until earlier this year. The Iraq-based part of the movement is likely to have been responsible for killing most of the 44 people shot dead or killed in bomb attacks and shooting in Iraq in recent days.

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Mr Hamami, also known as Abu Bassir al-Ladkani, was a member of the Supreme Military Council of the Free Syrian Army (FSA) and commander of an important brigade within the loosely-organised FSA.

A spokesman for the FSA said Mr Hamami had been driving through Latakia on his way to take part in an operation against regime forces when he encountered a checkpoint manned by members of the Islamic State of Iraq and the Levant. When the fighters from the al-Qa’ida-linked group refused to let him pass through, Hamami ordered them to dismantle their checkpoint. After they refused to do so, a confrontation ensued in which Hamami was killed.

It is not clear if his death was the result of that dispute or a pre-planned assassination, but the Free Syrian Army yesterday appeared to be convinced of the latter.

“We think they made a decision to fight us. It seems they have prepared themselves very well for this moment,” FSA spokesman Louay Mekdad, told The Independent.

“They have started to take control in certain areas and started to arrest certain people. We will not allow this to happen,” he added.

Mr Mekdad said that a video conference had been held between members of the FSA’s military council on Thursday to decide an appropriate response to the attack. A second crisis meeting was due to take place yesterday between General Salim Idriss, the commander of the FSA, and other rebel leaders.

The shooting may be the precursor of an all-out civil war between the Islamic State, whose in primary leadership is based in Iraq, and the FSA. Mr Mekdad says that one FSA fighter caught in the ambush was allowed to go free in order to carry a message from the Islamic State saying that it considers the FSA as heretics and will target its 30-member Supreme Council. He added that “if these people came to defend the Syrian revolution and not help the Assad regime, the they have to hand over the killers,” adding that the bodies of the two-men are still held by the Islamic State forces.

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FSA commanders reacted angrily to the killing. “We are going to wipe the floor with them,” one was quoted as saying, before adding that there was “no place” for al-Qa’ida type militants in Latakia province near the Syrian border.

The Islamic State of Iraq and the Levant was formed earlier this year and is made up of fighters who split from the al-Nusra Front. The split was prompted by an announcement by Abu Bakr al-Baghdadi, the leader of al-Qa’ida in Iraq, who claimed to have been responsible for founding al-Nusra.

In April, Mr al-Baghdadi announced a merger between al-Nusra and al-Qa’ida in Iraq, which would operate under his leadership. The merger was opposed by al-Nusra’s leader in Syria, Abu Mohammed al-Golani, and the fighters who had been operating under the al-Nusra umbrella broke into two groups under the two leaders. Those loyal to Mr Al-Baghdadi now operate under the name of the Islamic State of Iraq and the Levant.

The Islamic fundamentalists have been making headway within the opposition because they are better organised, fight harder, are well funded and less prone to loot civilian property. They also guarantee a degree of order in districts they control by implementing summary justice under Sharia law while the FSA units are notorious for plundering factories and warehouses and selling for profit humanitarian aid sent from outside Syria.

The US, Britain, France and their regional allies in Saudi Arabia, Qatar and Turkey have been continuously trying to boost the FSA and the Syrian Coalition, the civilian rebel opposition, as representative of Syria as a whole.

Despite the blows it is receiving from Islamic fundamentalists supporting the rebellion and from Syrian government forces the FSA is still hopeful of receiving US and European weapons and equipment. An opposition statement pledged that these arms would not fall into the hands of Jihadi fighters because “the Syrian Coalition and the Free Syrian Army have already introduced necessary measures to ensure full and comprehensive vetting of all armed forces under our command.” The killing of Mr Hamami is evidence that the FSA may be in no position to guarantee anything inside Syria.