Eleven Syrian rebel groups, including a powerful al Qaeda affiliate, have rejected the Western-backed opposition coalition, calling for a new Syria under Islamic law and dealing a severe blow to U.S.-led efforts to support a democratic alternative to embattled President Bashar Assad.

In a statement read out in an online video late Tuesday night, the rebel alliance called on other militants fighting to topple the Assad regime to unite under a “clear Islamic framework.”

“The prospect that the Islamists are going to be able to set up some sort of overarching political and military coordination and organizational structure should be troubling not only to the Syrian secular opposition, but also for Washington,” said David Schenker, director of the program on Arab politics at the Washington Institute for Near East Policy.

The rebel alliance rejected the leadership of Ahmad Saleh Touma, who earlier this month was elected the interim prime minister of U.S.-backed National Coalition of Syrian Revolution and Opposition Forces, also known as the Syrian Coalition. But it pointedly made no mention of Gen. Salim Idriss, head of the Supreme Military Council of the Free Syrian Army, the military wing of the political opposition. Gen. Idriss also serves as a conduit for foreign assistance to the rebels.

The rebels’ declaration also shunned “all groups formed abroad,” a reference to the Turkish-based Syrian Coalition.

“From an international perspective, the argument that we want to fund a moderate opposition has just been blown full of holes,” said Valerie Szybala, a Syria analyst at the Institute for the Study of War.

“The job of people like Gen. Idriss, who have been trying to gather support from Western countries, has been made impossible, if not extremely difficult.

“But you could also make the argument that he wasn’t really getting that job done anyway, so the brigades who joined made the calculation that that was a losing battle.”

The new rebel bloc includes some powerful factions of the Free Syrian Army, which is likely to undermine the case to arm and fund the moderate opposition. Obama administration officials said this month that U.S. arms had begun flowing to the Free Syrian Army.

The Obama administration was caught off guard by the announcement, and a U.S. official told The Associated Press that it is too early to determine what the impact will be. Another U.S. official said the U.S. and its allies are increasingly concerned about infighting between the Free Syrian Army and al Qaeda militants in northern and eastern Syria.

“We are discussing and have already begun discussing the impact of this announcement with our Syrian opposition counterparts,” a senior State Department official said on the condition of anonymity.

The statement was issued hours after a delegation from the coalition met with Secretary of State John F. Kerry in New York, and as a team of U.N. specialists arrived in Damascus to continue investigating the suspected use of chemical weapons in the civil war.

End of the Free Syrian Army?

Miss Szybala said the formation of the Islamist rebel bloc could deal a blow to the rebels’ moderate armed wing.

“I imagine there will be other brigades in Syria who are going to jump on this train and join this alliance unless foreign funders don’t like it and push back,” she said. “You may see this be the end of the Free Syrian Army. It is going to be hard for them to bounce back from this one.”

The new rebel alliance also may signal a rift between the two al Qaeda affiliates fighting in Syria. Jabhat al-Nusrah, also known as the Nusrah Front, has taken a lead role in the alliance, while the Islamic State of Iraq and the Levant has been left out. The Nusrah Front, which the State Department has listed as a terrorist organization, is also one of the most effective rebel militias fighting the Assad regime.

Extremist and more moderate rebel groups fighting Mr. Assad’s forces have increasingly turned on each other in recent months. Last week, fighters from the Islamic State of Iraq and the Levant defeated units of the Free Syrian Army and seized control of Azaz, a strategic town close to the border with Turkey.

Those Islamist rebels have the advantage of a steady supply of arms and money, thought to originate from Saudi Arabia and Qatar. As a result, they have increasingly outperformed the more moderate groups fighting the Assad regime since March 2011 in a war that the United Nations estimates has claimed more than 100,000 lives.

“The secular opposition is being overshadowed, in terms of performance, by these Islamist militias,” said Mr. Schenker. But these Islamist groups “have not, until now, really tried to translate their performance on the ground into a larger political framework.”

“So the Islamists, I think, came to the understanding that ‘Why not try and supplant or at least compete with these secular opposition groups politically?’” he added.

Other members of the new rebel alliance include the Tawheed Brigade, which is thought to be the largest rebel group in the northern city of Aleppo, and the 19th Division, which identifies itself as part of the Free Syrian Army.

“Most of the groups battling against Assad are composed of Islamist fighters, but only a small minority could accurately be characterized as extremist,” a U.S. official said on background.

The radicalization in the opposition’s ranks has been fueled, in part, by the Obama administration’s decision to shelve its plans to take military action against the Assad regime for using chemical weapons, say Western analysts and Syrian activists.

Backlash from Syrians

Many Syrians view the opposition coalition in Turkey as fractious and out of touch with the revolution.

Islamists, too, have faced a backlash from the local population as they have sought to establish control in the northern and eastern parts of Syria. While these groups have provided much-needed services, they have angered locals by seeking to impose Islamic law.

“The balance of power is such that these Islamist militias see themselves as ascendant and also see that their rivals aren’t really getting outside backing like they are,” Mr. Schenker said.

“So it really falls on us to wonder why we are not doing more to strengthen the more moderate opposition. We talk about them periodically, but we are doing precious little to advance their cause vis-a-vis their Islamist rivals,” he said.

President Obama, in a speech at the United Nations on Tuesday, pledged $340 million in additional assistance to Syria and reiterated his support for the moderate opposition. However, U.S. officials, who have to deal with a hodgepodge of rebel groups, are worried about the aid falling into the wrong hands.

A photograph circulating on the Internet purports to show a commander of the al Qaeda-linked group inside a shelter bearing the logo of the U.S. Agency for International Development. Karl Duckworth, a USAID spokesman, said he could not authenticate the photograph.

Since April, USAID has been providing heavy-duty plastic sheeting with the USAID logo to people displaced by the fighting who are living in “spontaneous camps” in northern Syria, Mr. Duckworth said. The war has displaced an estimated 5 million people within Syria.

Mr. Duckworth said armed fighters sometimes enter the camps, but “We have taken every precaution to ensure that humanitarian aid reaches those in need.”

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