Shashank Joshi: Minorities are rightly fearful as Islamists step in to fill power vacuum

Syria's regime is rapidly unravelling. In the same week as a bombing that killed four of President Assad's top security chiefs, rebels have seized control of the Syria-Iraq border and turned Damascus into a war zone.

Defections and assassinations have hollowed out the core of the regime. But Western states – having repeatedly demanded Assad's departure – are now worried about catastrophic success. If this week's bombing was a suicide operation then one concern is that battle-hardened jihadists are playing a greater role and could exploit the post-Assad chaos.

The Free Syrian Army insists it planted a remote-controlled bomb, which would suggest the bombing does not herald a campaign of attacks on ordinary civilians. But a group called the Brigade of Islam has also claimed responsibility, and hardline Islamists are undoubtedly active in Syria.

In January, a previously unknown group, al-Nusra Battlefront, claimed responsibility for bombs targeting security buildings. Al-Qa'ida's leader, Ayman al-Zawahiri, has also called on Muslims in Iraq, Jordan, Lebanon and Turkey to fight against Assad's "pernicious, cancerous regime". Al-Qa'ida has both the motive and opportunity to exploit Syria's fraught sectarian balance. In Iraq, Sunni fundamentalists attacked the majority Shia population and sparked off a civil war. In Syria, the danger is that revenge attacks on Assad's Alawite sect will prolong civil war.

The Syrian National Council has promised to resist such pressures. It affirms national unity and says it wants a "civil state", not a Sunni theocracy. The problem is these promises are rather flimsy.

The rebels' principal benefactor, Saudi Arabia, is hardly a model of sectarian harmony. Syria's Kurds don't trust the SNC because of its links to Turkey. And fearful Alawites will ask how the divided and weak SNC can hope to enforce these guarantees when it is estranged from the Free Syrian Army, the network of fighters on the ground.

This does not mean that a jihadist takeover is probable. Although Islamists dominate the opposition, outright jihadists are few. The latter may exact a terrible toll on minorities, but they cannot seize the levers of government. The greater problem is likely to be familiar from Libya: the presence of entrenched local militias, which challenge the authority of a weak central government.

Shashank Joshi is research fellow at the Royal United Services Institute