ISTANBUL—The Western-backed Free Syrian Army clashed with al Qaeda fighters in towns throughout northern Syria on Friday, drawing support for the first time from Islamic militants also fighting the Assad regime.

The fighting marked the first major, sustained clashes between two Islamist rebel groups that were to be allied: al Qaeda's Islamic State of Iraq and al-Sham, or ISIS, and the Islamic Front, a coalition of less-radical religious militias.

Just last month, the Islamic Front seized an FSA warehouse storing U.S. military gear. But Friday's fighting—pitting the Islamic Front and secular FSA against ISIS—signaled that alliances may be shifting.

Widespread public protests against ISIS on Friday also highlighted growing public resistance to the group whose mostly foreign fighters and heavy-handed tactics have stirred opposition among Syrians of all stripes.

Syrian rebels say that the ISIS fighters have hijacked their revolution, moving in on territory the FSA won in hard-fought battles against government forces and kicking out the secular opposition. ISIS jails and even executes Syrians who oppose their rule and goal to create an Islamic state.