Syria's war within a civil war as rebels turn on each other

Standing on a patch of muddy scrubland just inside Syria's broken border fence with Turkey, the rebel commander watched glumly as the group of jihadists crossed into his country.

Scruffy, with long beards, some wearing khaki jackets and each clutching a black travel bag, the six men walked silently through the crowd of refugees who were waiting to leave Syria. A driver in a pick-up truck greeted the men quickly and drove them away into the countryside.

"Libyans", muttered the rebel Free Syria Army leader under his breath, shooting the men a dirty look. "We don't want these extremist people here. Look at them; we didn't have this style in Syria - who is this? Bin Laden?"

Even before President Bashar al-Assad has been defeated, a war within the civil war is brewing in Syria. It is a battle of ideas, a struggle for the overall direction of the insurgency that is pitting moderate-Muslims against Salafists, jihadists and other Islamist groups.

Syria's most powerful Islamist brigades have united under a new "liberation front" to wage jihad against President Bashar al-Assad's regime and turn the country into an Islamic state.

After more than a month of secret meetings, leaders of Islamist fighters - including the heavyweight Farouq Brigade that operates mainly in Homs province and the influential Sukour al-Sham brigade of Idlib - have formed the "Front to Liberate Syria".

"We are proud of our Islamism and we are Islamists. We do not want to show it in a slogan because we might not live up to the responsibility of Islam", said the leader of the Front, Abu Eissa, "but we want a state with Islamic reference and we are calling for it".

In Syria's northern provinces of Idlib and Aleppo, these militant groups have grown in strength and in numbers, and now threaten to take over the revolution in this strategic part of the country. Driving along the winding lanes in the countryside of the "liberated" northern province of Idlib, the black Islamic flag often used by jihadists frequently flies at rebel checkpoints and on municipal buildings.

The refusal by western governments to provide cash or armed support to the rebel Free Syrian Army, which is leading Syria's secular opposition to the Assad regime, has put it at a disadvantage.

Resistance groups that adopt a more overtly Islamist hue are finding it easier to attract financial support from abroad. Religious fighting groups are the prime beneficiaries of money and weapons donated by the government of Qatar, as well by wealthy businessmen and religious leaders in the Gulf and Saudi Arabia.

Nor is the more secular Free Syrian Army helped in its struggle for financial support by the fact that it has attracted most of the defectors from the Assad regime. "Syrian defectors join the FSA, but people dislike them because they were once part of Assad's system," one observer told The Sunday Telegraph. "Donors would rather give money to people they know from their mosques, or from tribal family connections. Because of this the more religious Salafi groups attract a lot more funding from outside."

The growing strength of the Islamist groups has polarised the myriad of disparate rebels in Syria into two powerful rival factions: the Islamists and the moderate nationalists. In parts of Idlib province where the battle against the regime has been all but won, these factions are turning on each other.

The Sunday Telegraph accompanied the head of the Free Syrian Army Supreme Military Council, General Mustafa al-Sheikh, as he moved the FSA's command centre from Turkey to inside Syria. They travelled nervously through Idlib's countryside, in cars with blacked out windows, heavily armed, and with their rifles locked and loaded.

"It is not because of the regime that we are carrying weapons. We are afraid of being attacked by the jihadists," an FSA rebel later admitted.

Backed by millions of dollars of funding, much of it from Saudi Arabia, General al-Sheikh's men are creating a faction of moderate nationalists, working to turn the rebel fighting brigades from the Free Syrian Army into a disciplined national military. Rebel-training camps have sprung up across Idlib that attempt to instil discipline into their fighters. Religious connotations within the groups are being stamped out, with the names of individual fighting groups being replaced with "division" numbers.

"We are trying to set principles for a new constitution - both military and civilian," said Dr Kamal al-Labwani, a key opposition figure who fought against the regime for more than three decades and now advises rebel groups inside Syria and briefs western governments.

"This local council must start to work for a modern civilian state, and an impartial army. But now we will face the fanatics and Islamists. It will take time. We cannot ignore Islamists - I am afraid that they will rule Syria," said Dr Labwani.

Neither front is yet strong enough to fight both the Syrian regime and their rebel colleagues openly, but both sides try to choke the other's influence.

A group of jihadists, including 40 foreign fighters, were pushed out from the Bab al-Hawa border checkpoint after they kidnapped British photographer John Cantlie and Dutch journalist Jeroen Oerlemans, and sought to turn the area into an Islamic emirate. Two Britons were arrested last week at Heathrow Airport on suspicion that they may have been part of that group.

"They were acting as a gang, not as Muslims. They burnt buildings and tried to stop women that came through the checkpoint from driving cars," said the commander of northern Idlib division of Farouq brigade, calling himself Abu Zeid.

Secular rebel commanders also revealed that they are working to cut the supply lines of jihadist groups, and limit the influx of foreign fighters to their ranks.

"We watch the borders. If we find supplies entering for [jihadist groups] we will take them," said one secular FSA fighter. "We have also caught 25 foreign fighters trying to cross from Turkey. We gave them to the Turkish intelligence."

But moderates are angry that the head of the Free Syrian Army was based in Turkey for so long, saying it stripped him of any legitimacy among fighters who were dying inside Syria.