Known as fierce fighters willing to employ suicide car bombs, the jihadist groups now include more than 6,000 foreigners, counterterrorism officials say, adding that such fighters are streaming into Syria in greater numbers than went into Iraq at the height of the insurgency there against the American occupation. 

Many of the militants are part of the Nusra Front, an extremist group whose fighters have gained a reputation over the past several months as some of the most effective in the opposition. 

But others are assembling under a new, even more extreme umbrella group, the Islamic State in Iraq and Syria, that is merging some Syrians with fighters from around the world — Chechnya, Pakistan, Egypt and the West, as well as Al Qaeda in Iraq, the Sunni insurgent group that rose to prominence in the fight against the American occupation in the years after the 2003 invasion. The concern is that a new affiliate of Al Qaeda could be emerging from those groups. 

It was the fear of militants coming to dominate the opposition that caused the United States and its Western allies to hold off providing lethal aid to the Syrian opposition, at least until now. But as a result, counterterrorism analysts say, they lost a chance to influence the battle in Syria. Even Congressional supporters of the C.I.A.'s covert program to arm moderate elements of the Syrian opposition fear the delivery of weapons, set to begin this month, will be too little, too late. 

The stakes are high. American intelligence officials said this week that Ayman al-Zawahri, the overall leader of Al Qaeda in Pakistan, has had regular communications with the Nusra Front in Syria, reflecting how favorably the Qaeda leadership views the long-term potential for Syria as a safe haven. Juan Zarate, a former senior counterterrorism official in the George W. Bush administration, said that Syria lay in the center of an arc of instability, stretching from Iran through North Africa, and “in that zone, you may have the regeneration and resurrection of a new brand of Al Qaeda.” 

In Syria, the battle lines have hardened in recent months. The Syrian government, backed by Iran and Hezbollah, has seized new momentum and retaken territory in the south and east from the rebels. At the same time, power within the badly fractured opposition, numbering about 1,200 groups, has steadily slipped into the hands of the jihadists based in the northeast, where this week they seized a strategic airport in the area. They also hold sway in the provincial capital of Raqqa. 

The idea that Syria could supplant Pakistan as the primary haven for Al Qaeda someday, should the government fall, is a heavy blow to the Western-backed Syrian opposition and its military arm, the Free Syrian Army. It plays directly into the hands of Syria’s president, Bashar al-Assad, whose government has sought to portray itself as the only alternative to Islamic extremism and chaos, and has made the prospect of full-on American support even more remote than it already was. 

Mr. Assad’s argument “began as a fiction during the period of peaceful, unarmed protests but is now a reality” because of Mr. Assad’s own efforts to divide the country as well as the success of the extremists, Hussein Ibish, a senior fellow at the American Task Force on Palestine, wrote in a recent essay that appeared in The National. 

In Raqqa recently, a commander of the Islamic State in Iraq and Syria sipped coffee after breaking the Ramadan fast, wearing a Pakistani-style outfit. The commander, Abu Omar, was Syrian, a member of a tribe in the area, but he described his movement’s goals as reaching far beyond the country’s borders. 

He did not speak of attacking the United States. But he threatened Russia, and he spoke of a broad-based battle against Shiite-led Iran and its quest to dominate the region, and said Sunnis from across the world were justified in flocking to Syria to fight because of the government’s reliance on Shiite fighters from Lebanon and Iraq. 

He rejected calls from some in the Syrian opposition to keep the fighting focused inside Syria and aimed at toppling Mr. Assad. “We have one enemy,” Iran, he said, “and we should fight this enemy as one front and on different fronts.”  He also seemed to suggest that Russia would be a legitimate target for its role in supporting Mr. Assad and for its brutal suppression of Muslim militants in the Caucasus. 

“Russia is killing Muslims in southern Muslim republics and sends arms and money to kill Muslims in Syria as well,” he said. “I swear by God that Russia will pay a big price for its dirty role in the Syrian war.” 

The leader of the Free Syrian Army, Gen. Salim Idris, recently accused the jihadists of working for or receiving aid from the Assad government, not a completely far-fetched proposition, given that Western officials widely believe the Assad government played a major role in funneling Syrians and other foreigners into Iraq during the insurgency there. Some rank-and-file rebels say that government artillery and warplanes attack them fiercely while largely leaving jihadist positions alone. 

Free Syrian Army fighters have clashed with jihadist groups in recent weeks over weapons and supplies, and civilian anti-Assad activists have struggled with them over their efforts to impose religious rules on society. The groups have kidnapped and imprisoned dozens of activists. 

Yet the lines dividing the Free Syrian Army from jihadist groups are fluid, and the conflicts have not stopped F.S.A. leaders from working with their fighters, whose fierceness on the battlefield is undisputed. That has helped create a divergence between statements by exile opposition leaders rejecting extremists and their ideology and actions by ground commanders eager for any help they can get. 

“We are getting big accusations that we are implementing foreign agendas to divide the Syrian rebel groups or we are agents for the Assad regime,” Abu Omar said. “But we are the ones who made the big military operations against the Assad regime. When we fight any military position we get it or die for God’s sake.” 

This week, the jihadist group Jaish al-Muhajireen wal Ansar, or the Army of Emigrants and Supporters, led by a fighter from the Caucasus known as Abu Omar al-Shesheni — the Chechen — worked with Free Syrian Army battalions to take the Menagh air base in Aleppo Province after 10 months of trying. 

What appeared to turn the battle around, said Charles Lister, an analyst with IHS Jane’s Terrorism and Insurgency Center, were the relentless suicide vehicle bombings on the walls of the base — five or six times in the past two weeks, he said. 

After the battle, Col. Abdul Jabbar al-Okaidi, the head of the United States-backed opposition’s Aleppo military council, appeared in a video alongside Abu Jandal, a leader of the Islamic State in Iraq and Syria. 

In camouflage, Colonel Okaidi offered thanks to “our brothers al-Muhajireen wal Ansar and others,” adding: “We’re here to kiss every hand pressed on the trigger.” He then ceded the floor to Abu Jandal and a mix of jihadist and Free Syrian Army leaders, who stood together, each praising his men, like members of a victorious basketball team. 

Such cooperation has complicated efforts to isolate the jihadists within the insurgency, where commanders of all political stripes realize they have little choice but to collaborate with any ally available. 

“There’s an awful lot of pragmatism on the ground,” Mr. Lister said. “There’s a realization that without extensive coordination on the ground this could go on for years and years or the opposition could be defeated, so no matter what the long-term objective, it might be still worth it in the medium term to coordinate across groups.” 

But that same pragmatism, Mr. Ibish said, suggests there is hope that many of the Syrians fighting alongside extremists are not ideologically committed to those groups’ goal of an Islamic state, and could peel away from it if offered an alternative. 

The extremist ideology, he said, “runs counter to most traditional culture and lived realities of modern Syria, which is a heterogeneous and typically tolerant society.” 

Abu Omar, in Raqqa, laid out his vision for the future: women must cover their hair, but are not required to cover their faces; bars and nightclubs and eating during the Ramadan fast are forbidden.

“Everyone is free in his house but not free to break God’s law in public,” he said “The Shariah law is the best justice, not the Western democracy which gives us bad regimes like Assad’s.”