The Islamic State commands large swaths of territory in northern Syria, but it's never been a serious force in the south of the country — until now. Just two weeks ago a jihadist militia with allegedly close ties to the Islamic State or ISIS broke out of its isolated home base in the remote foothills of the Golan Heights, near Syria's border with Israel, seizing two major towns. In doing so, it linked up with territory controlled by a smaller hyper-extreme and Islamic State-sympathetic brigade operating nearby.

That's leading nationalist rebels to regret that they have left the jihadist groups unchallenged until they became a major threat — one that may have become too big to defeat without creating more, brutal rifts in southern Syria.

As the first group, Liwa Shuhada al-Yarmouk (the Yarmouk Martyrs Brigade), and the second, Harakat al-Muthanna al-Islamiyyah (the Muthanna Islamic Movement), joined forces and advanced, they effectively split in half the territory held by nationalist rebels in the southern province of Dara'a. That's a big deal for the Syrian rebels fighting to liberate the south from the regime of President Bashar al-Assad: they rely on a supply line that runs through the Jordanian border, and the jihadists' advance threatened to isolate them.

The two group's Islamic State links and sympathies have been known for months. In the early days of the Syrian civil war, Shuhada al-Yarmouk had initially branded itself as a nationalist faction of the Free Syrian Army rebel coalition, and even coordinated with US-backed rebel groups in the region. But its top leadership included long-time jihad veterans, and the group took an extremist turn around the end of 2014, when it added an Islamic State logo to its flag.

Muthanna – originally a splinter of Syrian al-Qaeda affiliate Nusra Front – was always a jihadist faction, but it reportedly became more extreme after the death of its founder in 2013. Then, in March of last year, it issued a statement conditionally affirming the Islamic State's legitimacy. In January, Muthanna was run out of eastern Dara'a after rebels accused it of engineering a wave of assassinations and abductions in the rebel-held south.

Though Shuhada al-Yarmouk's extremist bent had been common knowledge in Dara'a, the other rebel coalitions in the area — which are mostly affiliated with the nationalist Free Syrian Army — have left the jihadists alone until very recently, focusing their energies on fighting the Syrian government. And now that the jihadists have joined together in their part of Syria, the Free Syrian Army rebels say they are realizing it was a mistake to let the threat fester.

The black indicates the area of control by Islamic State-linked groups, green is rebel control, and red is Syrian regime control (Map via Agathocle de Syracuse)

These nationalist rebel groups rely on military support from the shadowy Military Operations Council in Jordan, a coordinating body that reportedly includes the CIA, Jordanian intelligence, and other regional intelligence services.

Rebel commanders told VICE News that they had warned their foreign backers that the jihadists were dangerous. "I let the Military Operations Council know that the Shuhada al-Yarmouk forces were increasing in number seven months ago," said a local rebel commander who asked to go by the pseudonym Abu Khaled so he could speak freely. "They were getting a lot of financial support and receiving a lot of weapons compared to the Free Syrian Army."

He said that the salary for a Free Syrian Army soldier is $30 a month, "not even enough for a pack of cigarettes," but Shuhada fighters got "$300 per person, plus $35 for his wife and for each of his children."

For the past three weeks, rebels have been fighting a village-by-village battle against the ISIS-linked groups in Dara'a. Though they've managed to keep their supply line open, al-Yarmouk and al-Muthanna still control significant territory in the Dara'a countryside. Each day brings a new round of fighting, and it's unclear who will come out on top.

Omar al-Hariri, local activist and spokesman for the Dara'a Martyrs Documentation Office, said that more than 50 fighters had been reported killed from all sides as of Tuesday night, although he suspected the real number was higher. And he said that as rebels fought the two Islamic State-linked factions, local civilians were caught in the middle.

"A number of civilians have been killed by the back-and-forth shelling between the warring sides," said al-Hariri. "The largest number of civilians were killed in the town of Jillin when Harakat al-Muthanna was in control of it. The factions that were trying to storm the town targeted it with mortars. The clashes also led thousands of civilians to flee to the plains, ravines and rugged territory around the towns where there were clashes."

Rebels who spoke to VICE News said they regretted letting the extremists in their midst fester for so long. "The battles happening now are the price of this complacency and leniency with extremism in the south," said Asmat al-Absi, head of the southern rebels' supreme court, which runs judicial affairs in the region. "That's how we got Shuhada al-Yarmouk and Harakat al-Muthanna, and if we're complacent again, we might get new [extremist] factions coming out."

"It was a mistake," said the rebel commander Abu Khaled, who also owns a farm on the front lines with these ISIS-linked forces. "A really big one."

As for why that happened, "we waited so long because we had no choice, militarily," said southern rebel commander Maj. Hassan Ibrahim, who also goes by Abu Osama al-Jolani. 'When you have more than one enemy, you can't open up more than one front at a time."

On top of that, rebels were leery of picking up an unwanted ally: Syrian al-Qaeda affiliate Nusra Front, which had been leading the fight against Shuhada al-Yarmouk for more than a year. Rebels were concerned that fighting alongside the Nusra Front might endanger their foreign backing – but also, they also just didn't like Nusra enough to pick a side.

"The local community rejected Nusra Front because of some unjust things it had done – some practices that weren't that far from what ISIS would do," said al-Absi, the judge. "So when the fighting started, people regarded it as two oppressors fighting each other."

Another reason the rebels may have waited is that their foreign backers wanted them to hold off and let the extremist groups fight amongst themselves. Some locals said the Jordan-based Military Operations Council, or MOC, discouraged rebels from fighting Shuhada al-Yarmouk, either by directly ordering them to stand down or by threatening to withhold supplies.

"The MOC operations room had pressured the factions of the Southern Front not to get involved on the grounds that it was a fight between two halves of al-Qaeda," said al-Absi.

"It was a decision made by the MOC," said Abu Khaled. "As a rebel group we're linked to the MOC. They're the ones who denied our request to fight these factions because at that time Shuhada al-Yarmouk denied that it was affiliated with and taking orders from Da'esh," the Arabic name of the Islamic State.

The CIA, the Pentagon, and the State Department declined to comment on what if any directive the MOC gave local commanders.

Rebel commander Maj. Ibrahim was vague about what advice he may have received from the MOC. He denied the MOC imposed a veto on fighting the extremists, but wouldn't say if he felt pressured to leave them alone. He instead emphasized that the rebels themselves preferred not to engage because they were busy fighting the regime and didn't want to be in league with the Nusra Front. He admits, however, that his men did "wait too long," and that now "they don't have any other option but to fight."

"It's either us or them," he said.

And now that his men are fighting against ISIS, he says they need more serious help from the US and its allies, and complains the international will just isn't there. While the Islamic State is subjected to a barrage of coalition airstrikes in the north of the country, Ibrahim and his men have no such support. "Airstrikes would be a dream," he says, "But all we really need is more money and weapons."

Rebels now say they won't stop until Shuhada al-Yarmouk and Muthanna have been dissolved and their members have put on trial. The mediation by local notables and clan elders that usually turns off infighting in the south has been called off.

But eliminating the two Islamic State-linked factions likely won't be easy. What is left of Muthanna has retreated to Shuhada al-Yarmouk territory, but Shuhada al-Yarmouk is defending its home turf. It is rooted in the Yarmouk Valley's clans and its fighters are the area's sons, many of whom won't surrender their farms and homes.

The Dara'a Martyrs Documentation Office's al-Hariri said he hoped that Shuhada al-Yarmouk and Muthanna could be forced into a negotiated surrender. The alternative, he feared, would be a cycle of blood revenge. "I expect it will be difficult to finish off these two factions," he said. "And if they're eliminated totally, then there will be revenge after-effects from [those factions'] members' relatives. Dara'a has a lot of overlap between clans and cousins."

Reem Saad contributed to this report.

Follow Avi Asher-Schapiro on Twitter: @AASchapiro