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The children of Abdel Salam, a Syrian rebel brigade commander, play with the fragments of rocket-propelled grenades recently fired at their father's men.Graeme Smith/The Globe and Mail

In the foggy hills near Syria's northern border, a band of rebels sits around a woodstove and makes dark predictions about how their uprising could turn into a religious war. Like most of the young men who joined the revolution, fighters from the Free Brigade all belong to the country's Sunni Muslim majority. They claim that their band of 200 men wants nothing except the overthrow of President Bashar al-Assad and his henchmen, not a massacre of the minority Alawite sect that dominates the government.

As the war drags into its second year, however, the fighters acknowledge that more extreme views are emerging among the other rebel brigades. They say regime forces are provoking sectarian feelings by spray-painting propaganda slogans on mosques, and Sunni religious scholars are calling for holy war. They acknowledge that a group of rebels in the Jabal Az-Zawiyah region of nearby Idlib province recently started calling itself the "al-Bara' ibn Malik Martyrs Brigade," using the name and flag of an al-Qaeda offshoot in Iraq.

For months, opposition activists played down the threat of Islamist groups within the Syrian rebellion, knowing that their presence made it harder to secure Western backing for their cause. However, some rebels are now speaking openly about the problem in their ranks, saying that the international community must act now to support the moderate opposition factions – before extremists take the lead.

"If the world is worried about a sectarian war in this country, they should do something quickly," said Abd al-Qader, 21, a former soldier from an air-defence unit who joined the rebels last year.

His own brigade is a case study in the way that Syria's protesters armed themselves, and illustrates how such improvised groups could integrate under a central command. The Free Brigade's members say their unit emerged last year under the leadership of a former taxi driver named Abdel Salam, from the port city of Latakia. The driver had no experience with war; unlike most Syrian men, he avoided military service because a childhood disease left him with one leg longer than the other.

Reached by phone at an undisclosed location inside Syria, the rebel commander said that he hasn't received any help from the Free Syrian Army (FSA), the group that claims to be organizing the armed resistance. His men have only Kalashnikovs and hunting rifles, he said, and a single rocket-propelled grenade launcher.

Unlike some other amateur commanders, however, Abdel Salam has accepted two FSA officers into his group to co-ordinate with the broader rebellion; he says more rebel brigades might do the same thing if the FSA could offer incentives of cash and arms.

Without that kind of structure to maintain order among the rebel brigades, Abdel Salam said, the rebellion risks slipping into outright war between the Sunni and Alawite religious groups.

"In these circumstances – killings, poverty, hunger, rapes – we have to resist and defend ourselves," the commander said.

The war increasingly pits the 74 per cent of Syria that is Sunni against the 12 per cent that is Alawite. The two groups have mistrusted each other for a thousand years, and the Assad regime appears to be trying to exploit that history, building a devoted cadre of Alawites who fear death if the government falls. Several Syrians said they had first-hand knowledge of security forces giving automatic rifles and other weapons to Alawite villagers.

Pro-government factions also appear to be deliberately provoking Sunni religious sentiments; refugees and rebels said they had seen regime slogans such as "No God except Bashar" written on mosques and buildings. Where protesters painted "No God except Allah," part of the traditional Muslim declaration of faith, security forces blasted the words with gunfire.

"They go into the mosques and insult us by smoking, or mocking our prayers," said Abu Abdo, 33, a stonecutter who escaped to Turkey with his wife and three children. Besides frightening Alawites into support for the regime, the hardening of sectarian feelings may be encouraging radical elements within the revolution – which, in turn, hurts the rebels' public image at precisely the moment when they are struggling for international recognition.

Some of the rebel brigades that grew famous in recent months have names that honour people allegedly killed by the regime: a lawyer, a poet, a 13-year-old boy. Other brigades honour secular heroes, such as an eighth-century Kurdish historian, or a Druze commander who fought against Ottoman occupation.

Some take their names from abstract religious ideas: there's the "Sword of Islam" brigade, and another whose name roughly translates as "Artillery of God."

More concerning for Western observers are the brigades whose names seem inspired by extremists.

Aaron Zelin, a researcher in the politics department at Brandeis University, noted in a Feb. 18 blog posting that a group of rebels had posted a YouTube video using banners in the background that strongly resembled a flag used by al-Qaeda in Iraq.

"Optics matter, which was why the al-Bara' ibn Malik Martyr Brigades were maybe more worrisome than others might be," Mr. Zelin said.

Al-Qaeda leader Ayman al-Zawahiri released a video in February calling on the faithful to support the Syrian rebels, and a White House spokesman recently said the United States is monitoring efforts by extremists "seeking to take advantage of the situation."

The Free Syrian Army appears to be making efforts to reduce the influence of brigades, trying to bring them under the authority of military councils based in each major city. Captain Ayham al-Kurdy, an FSA officer from central Syria, said the international community should not read too much into the emergence of the al-Bara' ibn Malik Martyr Brigades and similar groups.

"Every day we have new brigades," Mr. al-Kurdy said. "Of course our fighters are Muslim, so they name the brigades after their heroes. If we were American, we'd probably have a Michael Jackson Brigade."

The FSA has not won the confidence of many rebel fighters, however.

Mohammed, 35, a construction worker turned rebel who was shot in the leg during a skirmish on Feb. 21, said he trusts his local imams more than the FSA officers who take shelter inside the Turkish border.

"We are dying and wounded while they are sitting and eating," he said, referring to the FSA officers.

In early February, religious scholars in the Idlib area issued a fatwa instructing the faithful to take sides in the war. Such edicts have appeared elsewhere in the country since the early days of the revolution, but appear to be growing more common.

Some fighters said they view their struggle against the regime as a jihad, or holy war; many of them also said they consider the Alawites non-Muslims, even categorizing them as munafiqun, or hypocrites, who betray their claims to be faithful.

A 36-year-old farmer from Idlib, who brought his family to Turkey on Feb. 22, said that women from his village sold their gold jewellery so their families could buy Kalashnikov rifles at five times the usual price.

"The army wants to finish anybody who says ' Allahu Akbar,' " he said, referring to the common Islamic expression of faith. "They are destroying mosques. The rebels are mostly Sunni, so they are targeting Sunnis. … The Alawite officers say such bad words about Mohammed, Allah and Islam that I cannot repeat them."

Fingering a set of prayer beads, the farmer explained that from his perspective the conflict had already become a religious struggle.

"For us, jihad means defending yourself, your family, your religion," he said.

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