But rather than adopt the revolt's calls for democracy and the fall of a dictatorial regime, such jihadists believe the minority Alawite sect - an offshoot of Shia Muslims to which Assad's family belongs - are "apostates" and need to be fought and overthrown.
At the Bab al-Hawa border crossing with Turkey, seized by the rebel Free Syrian Army last week, dozens of men claiming to have travelled from several Arab and Muslim countries gather.
Some say they are from Algeria, others claim to be from Morocco, Saudi Arabia, the United Arab Emirates, Egypt, Libya and Tunisia. A few say they are from even farther away, including insurgent hotbeds such as Chechnya and Somalia.
From the start of the 16-month uprising - which has grown from a peaceful revolt into an armed insurgency - the Syrian regime has claimed rebels were hosting al Qaeda fighters, and that the revolt was a foreign conspiracy.
It is unclear just how many foreign jihadist fighters, have taken advantage of a growing gap in regime forces' control of the territory to enter the country.
What is clear is that Syria's rebels do not want to admit that the jihadist phenomenon exists.
In the central province of Hama, a rebel who identifies himself as Abu Ammar says he commands a 1,200-strong battalion.
"We will never let al Qaeda take root here - we'll kill them if they try," he says. "The revolution belongs to the Syrians."
But eyewitness accounts suggest those fighters are coming whether he likes it or not, some of them likely to have been spurred by militant websites urging militants to join the uprising.
One website, the World Jihad Network, features a call published by the Iraqi Banner of Right and Jihad in June 2012 to "volunteer for jihad in Syria."
Another carries a statement by Abu Bakr al-Husseini, identified as emir of the Islamic State of Iraq, an umbrella organisation for al Qaeda and proxy groups.
"I do not forget to pay tribute to our brothers in the blessed, beloved Syria," says Husseini, adding that "the Islamic state" does not recognise "artificial boundaries or frontiers."
The Lebanese militant group Fatah al-Islam, which is linked to Al-Qaeda, claimed responsibility in June for an attack on a military vehicle in the northern Aleppo countryside near the city of Aazaz.
"Thirty Alawite troops were killed in the Aleppo countryside," a statement from the group dated June 18 read, describing members of the Alawite sect as "Shia heretics."
In late April, Fatah al-Islam's leader Abdel Ghani Jawhar, one of Lebanon's most wanted men, was killed in Syria.
Jawhar was wanted by Lebanese authorities for the 2007 killing of 14 Lebanese soldiers in the northern port city of Tripoli.
Some believe that more jihadists will join the uprising as the fighting becomes more violent.
On one Internet forum, a statement by the Ansar al-Sham group says "the world needs to know that... Syria has started to attract young Arab men... who are ready to enter Syrian territory and join the revolutionaries and the fighters."
The statement adds that "no one has the right to blame the Syrians for the fact that Syria has become a theatre for international jihad."
The Ansar al-Sham statement also threatens attacks outside Syria.
"They have the right to target international interests the world over, belonging to whoever directly or indirectly supports the ruling gang in Syria."
"Hundreds of Libyan heroes" are also fighting against the "Nusayris" - a derogatory term used to describe Alawites - claims another Internet forum, Honein.
The forum shows a photograph of men wearing military clothing, and another of two protesters holding up a poster with a logo that reads "the Revolutionaries of (Libya's) Tripoli Brigade."
Not far from the Turkish border, in a village near the northern city of Aleppo, some 80 fighters have found a new home in what was once an administrative building.
Among them are Syrians, Turks, a Ukrainian, and two or three Chechens.
Well-organised and committed, the fighters prepare for battle as they engage in shooting drills in a nearby football stadium.
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The rebel fighters of the Free Syrian Army are too preoccupied with combating Assad's well armed forces that they don't worry about third forces like the Jihadists. Some even deny the presence of such groups inside Syria. The al Nusra in Syria, allegedly linked to the Al Qaeda has support from fighters, who had been on different battlefronts elsewhere before.
Religious extremist don't need much to justify killing - if they are so concerned about the Alawite sect running things why have they waited until now?
does killing one another bring some kind of thrill in these people.