Free Syrian Army fighters run with their weapons during clashes with forces loyal to Syria's President Bashar al-Assad at the Karam Barre frontline beside Al-Maysar neighbourhood of Aleppo on Nov. 2, 2014. (Hosam Katan/Reuters)

Fighters linked to al-Qaeda massed near a key Turkish border crossing Monday as they closed in on U.S.-backed rebels who were routed from their main bases in northern Syria over the weekend, in a major setback for Washington’s Syria strategy.

The gathering of fighters loyal to Syria’s al-Qaeda affiliate, Jabhat al-Nusra, raised fears that the militants intend to try to capture the Bab al-Hawa crossing, a strategically vital gateway to Turkey that has been a lifeline for more moderate rebels battling the Syrian government as well as the extremist Islamic State.

Whether the Free Syrian Army, an umbrella group of moderate rebels backed by the United States, will manage to survive the trouncing inflicted in recent days by Jabhat al-Nusra is in doubt. Two of the biggest rebel groupings in northern Syria have been scattered since their headquarters were overrun by Jabhat al-Nusra fighters on Saturday and Sunday, throwing the rebels into disarray and upending the Obama administration’s hopes for a moderate alternative to Syrian President Bashar al-Assad.

Many Free Syrian Army fighters have escaped toward the border area, where moderate rebels still hold ground, said Oubai Shahbandar, a spokesman for the Syrian opposition coalition.

“All is not lost,” he said, speaking by telephone from Istanbul. “The Nusra guys have made some pretty significant advances. But there are still FSA forces alongside the border. What happens in the next few days will be really crucial.”

The threat to the Bab al-Hawa border crossing echoes a recent assault on the Kurdish-Syrian border town of Kobane by the even more radical Islamic State, an al-Qaeda offshoot also known as ISIS or ISIL. That offensive became the focus of American airstrikes only after Islamic State fighters reached the edges of the town and Kurds appealed for international assistance.

Unlike Kobane, an obscure rural town that has been closed to cross-border traffic for decades, Bab al-Hawa is a major gateway between Syria and Turkey through which goods, people and supplies for the rebels flow.

Among those supplies have been modest amounts of U.S. assistance, including deliveries of nonlethal equipment such as trucks, food and medical supplies — both to rebel groups and to local councils run by the Syrian opposition.

U.S. officials said they did not know what, if any, U.S. assistance had fallen into the hands of the Jabhat al-Nusra rebels but that they were trying to find out. The officials refused to be identified and declined to comment further on the unraveling of the Syrian rebel groups on which the United States had pinned hopes for finding partners willing to fight the extremists, as well as Assad’s forces.

Moderate rebels who had been armed and trained by the United States either surrendered or defected to the extremists as Jabhat al-Nusra swept through the towns and villages they controlled in the northern province of Idlib, in what appeared to be a concerted push to vanquish the moderate Free Syrian Army, according to rebel commanders, activists and analysts.

Other moderate fighters were on the run, headed for the Turkish border as the extremists closed in, heralding a significant defeat for the rebel forces that Washington had been counting on as a bulwark against the Islamic State.

Moderates still retain a strong presence in southern Syria, but the Islamic State has not been a major factor there.

A senior Defense Department official said Sunday that the Pentagon “is monitoring developments as closely as possible” but could “not independently verify” reports from the ground. The official was not authorized to comment publicly and spoke on the condition of anonymity.

Jabhat al-Nusra has long been regarded by Syrians as less radical than the breakaway Islamic State faction, and it had participated alongside moderate rebels in battles against the Islamic State earlier this year. But it is also on the U.S. list of terrorist organizations and is the only group in Syria that has formally declared its allegiance to the mainstream al-Qaeda leadership.

A Jabhat al-Nusra base was one of the first targets hit when the United States launched its air war in Syria in September, and activists said the tensions fueled by that attack had contributed to the success of the group’s push against the moderate rebels.

“When American airstrikes targeted al-Nusra, people felt solidarity with them because Nusra are fighting the regime, and the strikes are helping the regime,” said Raed al-Fares, an activist leader in Kafr Nabel, in Idlib.

“Now people think that whoever in the Free Syrian Army gets support from the U.S.A. is an agent of the regime,” he said.

Fleeing rebel fighters said they feared the defeat would spell the end of the Free Syrian Army.

Among the groups whose bases were overrun in the assault was Harakat Hazm, the biggest recipient of U.S. assistance offered under a small-scale, covert CIA program launched this year, including the first deliveries of U.S.-made TOW antitank missiles. The group’s headquarters outside the village of Khan Subbul was seized by Jabhat al-Nusra overnight Saturday, after rebel fighters there surrendered their weapons and fled without a fight, according to residents in the area.

Hussam Omar, a spokesman for Harakat Hazm, refused to confirm whether American weaponry had been captured by the al-Qaeda affiliate because, he said, negotiations with Jabhat al-Nusra are underway.

Harakat Hazm, whose name means “Steadfastness Movement,” had also received small arms and ammunition alongside nonlethal aid in the form of vehicles, food and uniforms from the United States and its European and Persian Gulf Arab allies grouped as the Friends of Syria alliance. Scores of its fighters had received U.S. training in Qatar under the covert program, but it was also not possible to confirm whether any of those fighters had defected to the al-Qaeda affiliate.

Another Western-backed group, the Syrian Revolutionary Front, on Saturday gave up its bases in Jabal al-Zawiya, a collection of mountain villages that had been under the control of the pro-American warlord Jamal Maarouf since 2012. A video posted on YouTube showed Jabhat al-Nusra fighters unearthing stockpiles of weaponry at Maarouf’s headquarters in his home town of Deir Sunbul.

In a separate video, Maarouf, addressing the Jabhat al-Nusra leadership, said he fled along with those of his men who had not defected, “to preserve the blood of civilians, because you behead people and slaughter them if they do not obey you.”

The loss of northern Idlib province could prove a crippling blow to the moderate rebels, whose fight against Assad’s regime began in 2012 and has since been complicated by the rise of rival Islamist groups with goals very different from those of the original revolutionaries.

Idlib was the last of the northern Syrian provinces where the Free Syrian Army maintained a significant presence, and groups there had banded together in January to eject the Islamic State in the first instance in which Syrians had turned against the extremists.

Most of the rest of northern Syria is controlled by the Islamic State, apart from a small strip of territory around the city of Aleppo. There the rebels are fighting to hold at bay both the Islamic State and the forces of the Assad government, and the defeat in Idlib will further isolate those fighters.

Perhaps most significant, it will complicate the task of finding Syrian allies willing to join the fight against the Islamic State, said Charles Lister of the Qatar-based Brookings Doha Center.

“The United States and its allies are depending very strongly on having armed organizations on the ground to call upon to fight the Islamic State, and now those groups have taken a very significant defeat,” he said.

Suzan Haidamous in Beirut and Karen DeYoung in Washington contributed to this report.