LONDON – The Bab al-Hawa crossing post sits under a low ridge on the Syrian-Turkish border, not far from the Turkish town of Reyhanli. There is a concrete canopy and a handful of buildings. It is important because of what lies not far away in the village of Babisqa — one of the main storage depots for the Supreme Military Council of the Free Syrian Army.

In the Syrian conflict, who controls crossings like Bab al-Hawa and depots like Babisqa is crucially important.

On the evening of Dec, 6, a series of events began, with ramifications threatening to be far-reaching. They point to a development many observers have been fearing: a dangerous new fracture opening within the fragmented ranks of Syria’s opposition fighters, which threatens to pit the FSA against a powerful Islamist coalition. The ideological frontiers on the map of Syria’s civil conflict are shifting.

Accounts are confused and contradictory. But according to one version, members of a powerful new alliance of Islamist groups — the Islamic Front, which includes among its seven core groups some which in the past have cooperated with the al-Qaida-affiliated Jabhat al-Nusra — took control firstly of the warehouses at gunpoint, claiming they were defending them from an attack, and later the Bab al-Hawa crossing.

Within days, the U.S. and the U.K. had “suspended” all deliveries of nonlethal materials to the Supreme Military Council through Turkey. Although the FSA’s chief of staff, Salim Idris, and his aides have tried to play down the incident — claiming the warehouses were taken in agreement with him, and denying reports that he had fled the country — the events mark a worrying new turn. “The situation in the north now is very complicated and very dangerous, because there are some problems between some groups, and I think we should try everything to find a solution,” Idris said earlier this month.

His comments follow a warning he delivered last month to the U.S. broadcaster PBS, when he accused jihadi groups of “fighting against” the Free Syrian Army. “They are trying to control the territories, which we liberated before. And they don’t fight against the regime. And they are, for us, very dangerous.” And dangerous not simply because of their ambitions, but because the new Islamic Front can now muster about 45,000 fighters, three times as many as the FSA. In a conflict in which the tide has been turning in favor of President Bashar Assad, the balance of power has been shifting also among opposition groups, increasingly in favor of well-armed Islamists, some allied to al-Qaida and supplied by wealthy donors in Qatar and Saudi Arabia, at the expense of the FSA.

The shift comes amid warnings from counterterrorism experts that the two main al-Qaida-affiliated groups — Jabhat al-Nusra and the rival Islamic State of Iraq and Syria (ISIS) — are now better established in Syria and pose a greater threat than al-Qaida in Iraq at the height of its strength there in 2006-07. Writing in the journal of the Combating Terrorism Center at West Point, Brian Fishman argued: “Jabhat al-Nusra and the ISIS have more safe havens than [al-Qaida] had in Iraq. The Syrian military has been denied access to vast swaths of Syria for months. . . . Those safe havens mean that [the two groups] can mitigate their ideological extremism through better training, and foreign fighters can be vetted and trained more thoroughly because they are less of a security hazard than foreign fighters were in Iraq.” If the al-Qaida affiliates are better established and stronger than in Iraq, he argues, it is because they are not only not under pressure from a U.S. military presence, but also have learned from mistakes in Iraq, where they alienated much of the population.

Equally concerning for diplomats pushing for progress at next month’s Geneva II conference is that the alphabet soup of rival groups and individual brigades competing for territory and influence is making it ever harder to achieve consensus, not least because some Islamist groups have already rejected the conference. It is not simply the shifting fortunes for individual groups, as Fishman and other analysts have pointed out — their agendas also differ. While Jabhat al-Nusra is in the van of the fight against the regime, ISIS — analysts and rivals charge — has been more interested in consolidating its grip on territory it controls and establishing its own forms of governance.

The formation last month of the Islamic Front, a grouping that — on paper at least — has united tens of thousands of fighters from some of Syria’s most powerful Islamist groups has inevitably provoked suggestions that its emergence has undermined the authority and influence of the FSA. Although officially British and U.S. diplomats were insisting this month that the FSA — and Idris — were still the key force to be reckoned with, there were increasing indications that behind the scenes there is pressure to recognize the changing circumstances.

At one end of the spectrum has been the remarks of those like former diplomat Ryan Crocker, who has served in Syria, Iraq and Afghanistan, to The Washington Post, insisting that the U.S. will need to deal with Assad. “We need to start talking to the Assad regime again” about counterterrorism and other issues of shared concern, the paper reported, adding: “It will have to be done very, very quietly. But bad as Assad is, he is not as bad as the jihadis.” If Crocker’s advice is unlikely to be heeded, what is already happening, according to some, is discreet talks with more moderate groups in the Islamic Front, which reportedly took place in Turkey, headed by U.S. envoy Robert Ford, who traveled to London earlier this month to consult with other Western backers of the Syrian opposition, including the U.K. That intervention saw Syrian rebels announce that they were ready to include Islamist fighters as part of their delegation to the Geneva talks, another indication of their growing influence.

Senior rebel official Monzer Akbik told reporters in London that the opposition is “keen to form a delegation that will be as wide as possible,” and that the Islamic Front, an umbrella group of Islamist rebels, is welcome to send representatives.

Among those skeptical about the U.K. policy of backing the FSA as the key representative is Jane Kinninmont of the foreign policy think tank Chatham House. “I speak to people who say the role of the jihadis is exaggerated because of their strategy of capturing areas close to the borders to control arms and supplies, and who say the FSA is still stronger deeper inside the country. But the latest news is a bad sign. You get the sense the U.K. in particular is in a bit of a bind about having backed the FSA so strongly.” She argues that a number of other factors are converging that will make the conference more difficult, including the fury of Saudi Arabia over the U.S. nuclear deal with Iran. “Assad is making advances, he has presented himself as a partner with the West in getting rid of his chemical weapons, and is promising elections. With rising concern over the Islamist factions, and no prospect of outside military intervention, the levers that could be used to remove him are disappearing.”