The move adds to pressure on president Bashar al-Assad, facing a 30-month-old insurgency, but also undermines hopes of him being replaced by a pro-western regime.
Ever more divided on a battlefield where Mr Assad’s better armed troops have been gaining ground, allies of the Free Syrian Army (FSA) were among 13 rebel factions to disown the exile leadership and support an Islamic alliance that includes the al-Qaeda-linked Nusra Front, commanders said.
Details of the numbers of fighters involved and of how they would work together remained unclear. However, in an online video, a leader of the Islamist Tawheed Brigade said the bloc rejected the authority of the Syrian National Coalition (SNC) and the exile administration of Ahmad Tumeh, who is backed by the West and Saudi Arabia.
The split is likely to make it more difficult for western leaders to secure public support for military intervention. It could also jeopardise indirect support, which ranges from weaponry from the Gulf to non-lethal aid from Europe and the United States.
Meanwhile, a team of United Nations chemical weapons inspectors arrived in Damascus yesterday to continue investigating what officials have described as “pending credible allegations” of the use of chemical weapons in Syria’s civil war.
The visit of the six-member team, led by Swede Ake Sellstrom, follows a report by the inspectors after their previous trip in September, which said nerve agent sarin was used in a 21 August attack near the capital, Damascus.
Mr Assad was cheered by Russian diplomatic assistance that undermined US plans to bomb his forces in response to that attack. A more powerful rebel Islamist coalition could challenge his army’s resurgence, but that could be more than offset by a further weakening of international support for his foes.
Though some moderate Islamist fighters denied the move meant a more radical, sectarian approach, a more visible role for Islamist radicals at the expense of the SNC may bolster Mr Assad’s argument that the alternative to his rule, based on his father’s military takeover four decades ago, is a Syria run by al-Qaeda.
The most hardline Islamist faction, al-Qaeda’s Islamic State of Iraq and the Levant which has brought growing numbers of foreign jihadists into Syria, has not signed the new pact. It was unclear whether it had rejected involvement or had not been invited to join.
The 13 groups signed a statement calling for the opposition to Mr Assad to be reorganised under an Islamic framework and to be run only by groups fighting inside Syria. Signatories range from hardliners like the Nusra Front and Ahrar al-Sham to more moderate groups such as the Tawheed Brigade and Islam Brigade.
“These forces feel all groups formed abroad without returning do not represent them, so the forces will not recognise them,” said the statement read by Abdulaziz Salameh, leader of the Tawheed Brigade. “Therefore the National Coalition and its supposed government led by Ahmad Tumeh do not represent them and will not be recognised,” he said.
Analyst Aron Lund wrote on the blog Syria Comment: “If the statement proves to accurately represent the groups mentioned and they do not immediately fall apart again, it is a very big deal. It represents the rebellion of a large part of the ‘mainstream FSA’ against its purported political leadership, and openly aligns these factions with more hardline Islamist forces.”
Since the revolt began, Syria’s opposition has been riven by factionalism. There have also been tensions between Islamists and groups that support a secular vision for a post-Assad Syria.