Fears that the rebellion against the Assad regime is increasingly dominated by extremists has fuelled concerns in the West over supplying weaponry that will fall into hostile hands. These fears contributed to unease in the US and elsewhere over military intervention.
Charles Lister, author of the analysis, said: "The insurgency is now dominated by groups which have at least an Islamist viewpoint on the conflict. The idea that it is mostly secular groups leading the opposition is just not borne out."
The study is based on intelligence estimates and interviews with activists and militants. Two factions linked to al-Qaeda, Jabhat al-Nusra and the Islamic State in Iraq and the Levant (ISIL), have come to dominate among the more extremist fighters, Lister said. Their influence has risen significantly in the past year.
"Because of the Islamist make-up of such a large proportion of the opposition, the fear is that if the West doesn't play its cards right, it will end up pushing these people away from the people we are backing," he said.
"If the West looks as though it is not interested in removing Assad, moderate Islamists are also likely to be pushed further towards extremists."
Though still a minority in number, ISIL has become more prominent in rebel-held parts of Syria recently. Members in northern Syria have sought to assert their dominance over the local population and over the more moderate rebel Free Syrian Army (FSA).
Last week fighting erupted between ISIL and two of the larger moderate rebel factions, while al-Qaeda has assassinated several FSA commanders in northern Latakia province in recent weeks in what locals say is part of a jihadist campaign to gain control of the territory.
As well as being better armed and tougher fighters, ISIL and Jabhat al-Nusra have taken control of much of the income-generating resources in the north of the country, giving them significant economic clout, allowing them to "win hearts and minds" by providing food for the local population in a way that other rebel groups cannot.