For much of Syria’s civil war, Jordan has quietly supported the rebels fighting to topple the regime. In recent months, various coalitions of rebel forces have scored major battlefield gains, seizing towns and villages from the regime in the north and south of Syria.

But far from cheering these advances, Jordan is ready to pull the plug on the rebels.

Alarmed by the strength of Islamist militants in the rebels’ ranks and their recent seizure of a critical Jordanian border crossing, officials here say their priorities have changed from unseating President Bashar al-Assad to taking the fight to jihadists, including the self-declared Islamic State.

Now Jordan wants to train thousands of tribal fighters in eastern Syria, potentially opening up a new front against IS, also known as ISIS. This strategy dovetails with the US-led campaign to defeat IS in Iraq and Syria, with Assad’s dictatorial regime as a lesser priority.

The biggest loser from Jordan’s 180-degree shift in policy appears to be the Free Syrian Army, a secular group led by Syrian army defectors that Jordan, and the US, has trained and armed. And it comes, ironically, as the FSA, long derided as splintered and ineffective, is starting to make headway against Syria’s regime – but only by teaming up with Islamist militias deemed a threat to Jordan.

“There is a fear and frustration in Jordan that rather than moderate forces, support for the rebels in the south has only strengthened extremist groups such as Al Qaeda,” says Hassan Abu Haniya, a political analyst and expert on jihadist movements.

“There is an opinion that after four years, Syrian rebels can no longer be counted on.”

The US has also cooled on working with the FSA, even as the Pentagon rolls out a training program for vetted Syrian rebels as part of the Obama administration’s anti-IS policy. In recent months, US military officials have distanced themselves from the FSA. They say the training is open to “candidates from recognized groups” but won’t confirm if the FSA is among them.

The US goal is to train 5,400 “moderate” Syrian forces in Saudi Arabia, Turkey, and Qatar. Some 400 “are ready to proceed to the next screening and vetting stage prior to commencing training,” says Cmdr. Elissa Smith, a Pentagon spokesperson.

Border crossing under militants' control

On April 4, a coalition of rebel forces captured the Nassib crossing between Jordan and Syria, the last lifeline between the two countries, as part of a wider campaign for control of southern Syria. That campaign’s success, as well as major rebel gains in northern Idlib Province, has rattled Damascus and fueled talk of cracks in the Assad regime.

But Jordanian officials were alarmed when it became clear that rather than the FSA, Jabhat al Nusra, Al Qaeda’s branch in Syria, had taken over the border crossing. For the first time, Syria jihadists had reached Jordanian soil.

Jihadist sources say Nusra fighters in southern Syria number roughly 10,000, compared to some 60,000 FSA fighters. But while the FSA has larger numbers, it relies on Nusra’s superior weaponry during joint operations such as the capture of the border crossing from Syrian regime forces. Nusra fighters have also been on the front line in rebel offensives in Idlib.

According to FSA commanders, since the border seizure, travel between Jordan and Syria has become “difficult” and prominent FSA commanders have been prevented from returning to Jordan.

“The border remains closed and our forces are being left to fend for themselves,” says Assad al Zoubi, commander of the FSA’s southern forces. According to Zoubi, the rebel forces receive “minimum” financial aid from Saudi Arabia, which along with Turkey and Qatar has been a reliable backer of anti-Assad fighters.

It’s unclear to what extent Jordan’s policy shift could blunt the FSA’s momentum in Syria. For the last three years it afforded the FSA nearly unfettered movement of arms and fighters, while a large portion of the FSA command is based in Jordan, including Zoubi. Jordan played host to the training of FSA officers, reportedly by the CIA, and turned a blind eye to rebel recruitment in Syrian refugee camps.

Measured support for militias

Nick Heras, a research associate at the Center for a New American Security in Washington, says that unlike some regional powers seeking to depose Assad by proxy, Jordan took a measured approach in its support for insurgents.

“Very early on, Jordan didn’t make promises to the rebels. It forced them to demonstrate their intent. It didn’t put the rebels on a pedestal,” he says.

Over the past year, Jordan has begun to put a much higher priority on containing jihadist movements in Syria than on defeating the Assad regime. Jordan’s official position is that it supports a “political solution to end the violence” in Syria.

Observers and officials say Washington’s focus on fighting Islamic State is one factor in the policy shift. Jordan is a major recipient of US military aid and a partner in the aerial bombing campaign against IS. A Jordanian pilot captured last December by IS during a mission was later burned alive inside a cage by militants, enraging Jordan’s public and its ruler, King Abdullah, who vowed to step up the fight against IS.

The other factor is growing unease among Jordanian officials that aid and arms to moderate Syrian groups are falling into the hands of jihadist forces.

“Jordan’s new main priority and the US’s main priority is fighting terrorism, namely ISIS,” says Jawad Anani, a Jordanian senator and former foreign minister. “Jordan no longer wants to be drawn into supporting any side in this [Syrian] conflict.”

Tribal allies against IS

Now Jordan is turning to Syrian tribes and other social forces that have not been corrupted or tainted by ties with jihadist movements.

In what could become a plank of the US-led campaign against IS, Jordan is reaching out to Syrian tribes and civilians. It’s offering support in their fight to regain towns and villages overrun by IS – a preemptive step to prevent jihadists from threatening Jordan’s borders.

“We are helping Syrian civilians and tribes in the Eastern region to take back their towns and villages that have been taken over by ISIS,” says Mohammed al-Momani, Jordanian government spokesman and minister of media affairs.

“This is a new, international effort to help the Syrian people and is part of the war on terror and terrorist organizations.”

US defense officials declined to comment on Jordan’s training program for tribals. Jordanian officials insist that their strategy already has buy-in from the US and other allies, who are keen to find potential partners in Syria willing to fight against Islamic State.

Jordanian officials hope tribal forces would be more reliable than the FSA and other forces that have come to rely on the better-armed jihadist militias. They argue that tribal structures are easier to manage from afar, and that tribal sheikhs have the authority to lead the fight and not succumb to the internecine politics that hobbled the FSA.

Islamic State has also made inroads into tribes in eastern Syria, both by coercion and by inspiration. In what may be a nascent US strategy, Jordanian officials reckon that playing to tribal affiliations in Syria could encourage defections and weaken IS’s hold over the population.

Jordanian officials refuse to go into detail on the scope and timing of the training, citing security concerns. However, Syrian tribal sources claim they have been approached by Jordanian security services to provide “thousands” of potential fighters to take part in the training. As many as 5,000 tribal fighters and civilians could be involved, and tribal leaders have been offered the backing of coalition air power.

Talks have not, however, broached the issue of weapons supplies.

“We have 50,000 tribal fighters ready and willing to secure the borders in Iraq and fight extremist groups,” says Mohammed Azzab Al Darwoush, member of the Syrian Tribal Council and patriarch of the largest tribe in Homs. While IS doesn’t control Homs, it has strongholds around the town and controls its arterial roads.

“But we need weapons to break free from the Islamic State’s hold,” says Mr. Darwoush, one of several Syrian tribal leaders reportedly approached by Jordanian authorities.

Saudi distraction in Yemen

Saudi Arabia, an ally and financial backer, has long used Jordan as a rear base for anti-Assad rebels. With Saudi Arabia embroiled with the conflict in Yemen, government insiders say Jordan is no longer under pressure from Riyadh to back rebel forces, including the FSA.

“For Saudi Arabia, Syria is no longer a top priority. There is no longer a push to back sides in a conflict which seemingly has no end,” says Samih Maaytah, a former Jordanian minister of media affairs who remains close to the decision-making process.

Saudi observers and military insiders say Syria is no longer the “priority” for the House of Saud; a greater concern is how to “stabilize” Yemen before increasing support for Syria rebels. “Right now the priority for Saudi Arabia first and foremost is Yemen,” says Hani Wafa, political editor of the pro-government Al Riyadh daily.

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And that means that Jordan has greater flexibility to put its own security concerns – primarily, keeping jihadists in Syria and Iraq at bay – ahead of fealty to anti-Assad rebels. “Alliances in Syria have shifted over the past six months, and Jordan is moving with it,” says Mr. Maaytah.

Staff writer Anna Mulrine contributed reporting from Washington.