The Muslim Brotherhood has established its own militia inside Syria as the country's rebels fracture between radical Islamists and their rivals, commanders and gun-runners have told The Daily Telegraph.

Calling itself the "Armed Men of the Muslim Brotherhood", the militia has a presence in Damascus as well as opposition hot spots like Homs and Idlib. One of their organizers, who called himself Abu Hamza, said that he started the movement along with a member of the Syrian National Council (SNC), the opposition alliance.

"We saw there were civilians with weapons inside, so we decided to co-operate with them and put them under one umbrella," he said.

Hossam Abu Habel, whose late father was in Syria's Muslim Brotherhood in the 1950s, said that he raised $40-50,000 a month to supply Islamist militias in Homs province with weapons and other aid.

The militias he funded were not affiliated to the Free Syrian Army (FSA), the main rebel movement, added Mr Abu Habel.

"Our mission is to build a civil country but with an Islamic base," he said. "We are trying to raise awareness for Islam and for jihad."

The Syrian wing of the Muslim Brotherhood has been revitalized by the organization's success in Egypt, where it won both parliamentary and presidential elections.

In the early days of the uprising against President Bashar al-Assad, secular and Islamist rebels were both prepared to fight under the FSA's banner and recognize the SNC as their political masters.

But the FSA, dominated by defectors from the regime's army, has fallen out with the SNC, whose leaders are in exile. It now has its own political front, the Syrian Support Group (SSG). This split has divided the revolution's main international backers, with Saudi Arabia supporting the FSA and Qatar moving closer to the SNC and the Islamist militias.

The divisions are affecting operations on the ground: competing militias co-operate when necessary but otherwise disavow each other. "I would take it as an insult if you described me as FSA," said Abu Bakri, a front line commander of an Islamist militia in Aleppo calling itself the Abu Emara Battalion.

One activist described how he was working with Sunni politicians in Lebanon to buy arms for the FSA with Saudi money.

A member of the FSA command center, located in neighboring Turkey, told the Daily Telegraph that they have this week received large consignments of ammunition, machine guns and anti-tank missiles. At one point Saudi Arabia and Qatar were both funding the FSA, with the command center receiving up to $3 million in cash every month. But the operative said the situation had changed.

"Now we are not working with the Qataris because they made so many mistakes supporting other groups."

But the fracturing of the armed opposition raises the prospect of post-Assad Syria becoming a battleground. "This adds to the fragmentation and tones down the credibility of the opposition," said Louay Sakka, the SSG's Executive Director. "Supporters should go through the proper channel of the Free Syrian Army military council rather than build their own militias."

Amr al-Azm, a Syrian-American academic who was briefly on the SNC, said that Syria risked the same kind of disintegration that was set in motion by Saddam Hussein's downfall in neighboring Iraq. The West's decision to limit its involvement in the Syrian conflict – and refrain from supplying lethal weapons – had left a gap for the Islamists to fill.

"By playing to your own fears, you are making them come true," said Mr Azm. "By not intervening, you are forcing people to go those who have resources. No one wants to go to al-Qaeda, but if you are down to your last five bullets and someone asks you to say 'Allahu Akbar' (God is greatest) five times, you do it."

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