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 disparate rebel factions to disown the exile leadership and support an Islamic alliance that includes the al Qaeda-linked Nusra Front.
Details of the numbers of fighters involved and of how they would cooperate remained unclear. But, 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 Western and Saudi-backed exile administration of Ahmad Tumeh.
It is a setback for foreign leaders trying to bolster more secular rebel groups and to reassure voters sceptical of deeper involvement in Syria's civil war. Some may think again about help for the fighters, which ranges from weaponry from the Gulf to non-lethal aid from Europe and the United States.
For Mr Assad, already cheered by Russian diplomatic assistance that undermined US plans to bomb his forces following a poison gas attack, any more powerful rebel coalition could challenge his army's resurgence in the field. But that could be more than offset by a weakening of international backing for his enemies.
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 militant faction, al Qaeda's Islamic State of Iraq and the Levant (ISIL) which has brought growing numbers of foreign jihadists into Syria, was not a signatory to the new pact. It was unclear, however, 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 that all groups formed abroad without returning to the country do not represent them, so the forces will not recognise them," said the statement read online by Abdulaziz Salameh, the political 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."
Meanwhile, a team of UN chemical weapons experts, led by Swedish expert Ake Sellstrom, arrived in Damascus yesterday to continue investigating the use of chemical weapons.
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