ISTANBUL: The rise of Islamist groups of various stripes has changed the face of Syria’s war, leading to conflicts between those who back the uprising against President Bashar Assad but have differing versions for the country’s future.

Salafist groups now control much of the territory the regime has lost, leaving in the dust the activists who began their rebellion peacefully: online, in graffiti and through demonstrations.

When the United States deemed the powerful Nusra Front a terrorist organization in December of last year, the Islamist presence among the rebels took many outsiders by surprise. But it was the Syrian regime itself that played a major role in their genesis.

After the U.S.-led invasion of Iraq, Assad’s regime recruited around 3,000 religious Sunnis to organize jihadi militias and take their fight to the embattled country. When they returned, many were imprisoned in the suburban Damascus Sednaya Prison.

It was in these jail cells, where the regime violently put down a summer 2008 rebellion, that five groups combined under the name of the Syrian Liberation Front.

The front included: Fajr al-Islam, led by a doctor who fought in Iraq; Kataeb al-Haq, headed by a blind fighter named Abu al-Farouq; Suqour al-Sham, commanded by a man known as Abu Issa; Ahrar al-Sham, whose leadership is unknown; and Al-Tawhid Battalion, the military arm of the Muslim Brotherhood led by Abdel-Qader Saleh.

Assad ordered the release of the Islamist prisoners some two years ago, shortly after the uprising in Deraa, and the Syrian Liberation Front took to the battlefield, believing peaceful demonstrations would not be enough.

During the initial battle for the central city of Homs in 2011, the five groups came to the fore, although they were later pushed into the background by the Nusra Front, which announced itself with a series of dramatic bombings in Damascus last summer.

The Nusra Front, with its much discussed ties to Al-Qaeda, was formed from the Syrian Liberation Front’s Ahrar al-Sham, as well as the Al-Ouma Brigades and the Ahrar Deir al-Zor Battalions. It is led by Abu Mohammad al-Julani, who some have said is a Jordanian related to the slain senior Al-Qaeda figure Abu Musab al-Zarqawi. Others claim he is a Syrian Salafist from Damascus.

There are now an estimated 80,000 Syrian Islamist fighters engaged in battle, as well as approximately 18,000 foreign Islamist militiamen, according to sources. This includes some 2,000 fighters who are members of the Uighur ethnic group, a Muslim minority of Turkic heritage who live mostly in China.

The Nusra Front, along with several other Islamist groups, have designs on turning post-revolution Syria into an Islamic caliphate.

Fadel al-Salim, a lawyer who is close to the Nusra Front, told The Daily Star: “We are working to re-establish the Islamic caliphate in Syria, and we have informed [Syrian National Council head] Moaz al-Khatib that we will not accept the building of a civil state in Syria. We control the ground and will rule by Islamic law.”

The Nusra Front’s ties to Al-Qaeda and its hopes for an Islamic caliphate have made Western countries skittish, and are one of the major concerns cited with regard to arming the rebels.

Syrian opposition member Ibrahim al-Zoabi even spoke of meetings with U.S. officials who distinguished between “good” and “bad” Salafists, and indicated weapons supplied should only make it to the favored stream.

In another complication, Turkey’s current moderate Islamist leadership shares an ideological grounding with the Muslim Brotherhood’s militias.

Qatar too tends to favor the Brotherhood and its vision of a future Syria, which has led Saudi Arabia, with whom it has a rocky relationship, to support Salafist fighters like the Nusra Front. Saudi Arabia has long believed the Brotherhood to be a danger to their Wahhabi version of Islam, as well as their power in the Muslim world.

A member of the Syrian opposition cited Saudi Arabian concerns that the Brotherhood would take over Syria after the fighting finished, as they did in Egypt. He said divisions between those who support the Salafists and those who back the Brotherhood were clear in the ranks of the Syrian opposition.

But Syrian opposition member Sheikh Salim al-Mousallet believes none of these concerns are strong enough to defend the West’s hesitance to arm the rebels. “We would rather criticize those who give speeches in support of us but don’t support us on the ground than criticize Russia and China for their position on the Syrian crisis,” he said.