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BEIRUT — The assassination of a Syrian rebel fighter linked to al-Qaida called new attention Thursday to the ideological differences among the Islamists fighting the government of President Bashar Assad and threatened to set off new strife among the rebels.

The mystery surrounding the fighter’s death has opened a new window among the rebels, loosely allied as the Free Syrian Army, at a time when uncertainty about the opposition’s unity and character — in particular, the potential inclination toward intolerant or sectarian Islamist politics — has deterred the West from more muscular support for the cause of Assad’s ouster.

The fighter, Abu Mohamed al-Shami Abu al-Absi, led a brigade known as Jubhat al-Nusra, which calls itself an al-Qaida affiliate. His body was found Wednesday in an area known as Sarmada on the Turkish border, several rebel fighters said in interviews over the Internet. All said he had disappeared three days earlier and was evidently kidnapped and assassinated.

His killing aroused calls for revenge from his family as well as the group of Islamist brigades operating in the area, known as the Islamic Shura Council, in which he also played a leading role.

Some quickly pointed the finger at a major fighting group based in Homs, Al Farouq Brigade, which is considered Islamist but is opposed to al-Absi’s hard-line ideology. Brigades often collaborate on specific actions or fights, but each typically reports to its own leader.

“There has been tension between Al Farouq fighters and the rebels from the Shura Council,” said the commander of another brigade in the area, speaking on the condition of anonymity for his safety.