(CNN) -- Influencing events in Syria just got a lot harder for the Obama administration and its allies. Despite receiving months of training, diplomatic support and aid from the West, the Free Syrian Army's command has lost control of its headquarters and supply depots in northern Syria to the recently formed Islamic Front -- another sign that the balance among rebel forces is tipping toward militant groups away from more secular brigades.
The warehouses -- belonging to the FSA's Supreme Military Command (SMC) -- are at Bab al Hawa, a border crossing into Turkey. There are conflicting reports about just how they were taken over and what they held. The head of the SMC, Gen. Salim Idris, told CNN that only food and other humanitarian supplies were taken; other FSA officials say guns and two tons of ammunition were removed.
Turkish authorities closed the Bab al Hawa crossing after the Islamic Front occupied the Syrian side. Different Islamist militant groups now control several areas along Syria's border with Turkey, making the resupply of the SMC more difficult.
The Islamic Front was created last month by seven groups with the aim of toppling the regime of Syrian President Bashar al-Assad and creating an Islamic state in Syria "where the sovereignty of God almighty alone will be our reference and ruler." Two weeks later the Front abandoned the Supreme Military Command.
Aron Lund, editor of the Carnegie Endowment's Syria in Crisis website, says the Front includes some of the strongest rebel groups in Syria -- especially in the north.
"Most of these groups are concentrated in a particular area, like Aleppo or Damascus, but together they have units all across the country," Lund told CNN.
It is difficult to know how many fighters the Islamic Front includes, but estimates vary between 40,000 and 50,000, which would probably make it the single largest rebel command. In terms of ideology, the Islamic Front groups keep their distance from the strongest al Qaeda affiliate active in northern Syria, the Islamic State of Iraq and al-Sham (ISIS).
Even so, says Aron Lund, the Front "are hardline Islamists influenced by the Salafi school of thought. They want a theocratic state, and are opposed to secularism and Western-style democracy -- although they've said they can imagine having some sort of elections in a framework of Sharia law."
The most effective of the groups is Ahrar al Sham, which has been involved in the insurgency since its early days. Observers say it is disciplined and well-funded from Gulf sources and has captured a good amount of heavy weaponry, including tanks and mobile artillery, from government forces. Opposition activists say it was Ahrar al Sham that led the takeover of the SMC's headquarters at Bab al Hawa.
On the battlefield Ahrar al Sham and others in the Islamic Front groups do cooperate with another al Qaeda affiliate: Jabhat al Nusra. Some analysts say this is because al Nusra is more focused on waging the insurgency on a national level against al-Assad than is ISIS, which is devoting much of its effort to creating a mini-state -- an emirate -- in northern Syria, complete with Sharia law.
The leader of Ahrar al Sham, Hassan Aboud Abu Abdullah al-Hamawi, has been complimentary about al Nusra, telling al Jazeera earlier this year that "we see honesty in their work as well as toughness and courage."
The two groups joined forces to seize a border crossing with Jordan in September. But there are also instances, especially around Damascus recently, where fighters from the Front, al Nusra and ISIS have all fought together against al-Assad's forces. As so often in Syria, there are few hard-and-fast alliances and many local variations on a theme.
Valerie Szbala at the Institute for the Study of War in Washington says the Islamic Front contains a wide spectrum of groups, but for the West the presence of Ahrar al Sham -- and its extensive relationship with al Nusra -- is the most troubling. She says most of its funding appears to come from sources in the Gulf, especially Saudi Arabia.
Lund -- a contributor to the Sentinel journal of the Combating Terrorism Center at West Point -- says that because the Front is a new coalition "it is hard to tell how effective and organized it really is. The Islamic Front leadership has said that they are aiming for full unity, meaning that they want to merge all the member factions into one single group under one single leader, but so far it remains an umbrella organization."
For now, the Front's nominal leader is Ahmed Issa from Suqour al-Sham -- one of the more moderate but militarily one of the weaker components of the alliance.
For the last year, the United States and Britain have focused their efforts on building up the Supreme Military Command under Gen. Idris. But Idris has never been able to exert control over brigades with different local agendas, tactics and allegiances. Some have gained a reputation for smuggling and other crime rather than fighting the al-Assad regime.
Islamist factions have gained ground at the expense the Free Syrian Army -- sometimes with ruthless tactics. One senior FSA commander was murdered by ISIS in July. Another, Abdel-Jabbar Ukaidi, quit as head of the Aleppo Revolutionary Military Council last month. Ukaidi accused other commanders of in-fighting and building power bases rather than attacking regime forces, and had scathing words for the political opposition in exile. Other groups affiliated with the SMC -- such as Liwa al-Tawhid, Liwa al-Islam, and Suqour al-Sham -- lost faith and invested in other alliances.
Some analysts say the formation of the Islamic Front may be a double-edged sword. On the one hand, it is weakening an already dispirited FSA. But it may also draw Islamists away from al Qaeda affiliates, especially from ISIS. Valerie Szybala says as yet there is no evidence of that but she believes the Islamic Front may try to begin providing the sort of services that ISIS does -- including opening bakeries and handing out aid -- to win civilian support.
Alliances among rebel factions in Syria have come and gone with bewildering rapidity over the past two years, and it's far from clear how the Islamic Front will evolve. But a month before the Syrian government and opposition are due to meet under U.N. auspices in Geneva, the emergence of the Islamic Front complicates the most critical question: Just who is the Syrian opposition?