This July 9, 2013 citizen journalism image provided by Aleppo Media Center AMCshows Syrian rebels running during heavy clashes with Syrian soldiers in the Salah al-Din neighborhood of Aleppo, Syria. (AP)

Syrian rebels said Friday they would retaliate for what they described as the assassination of one of their senior commanders by an al-Qaeda-affiliated group, threatening to widen a rift between moderate and jihadist opposition forces fighting to topple President Bashar al-Assad.

The killing of Kamal Hamami, a member of the Western-backed Free Syrian Army’s top executive body, comes amid heightened tensions on the opposition side as jihadist groups extend their influence in rebel-held areas of northern Syria. Rebels said that Hamami, whose nom de guerre is Abu Bassir al-Ladkani, was shot dead Thursday in the coastal province of Latakia by gunmen from the Islamic State of Iraq and the Levant.

With the rebel forces struggling to fend off Assad’s troops in the central city of Homs, infighting among their disparate factions could play to the government’s advantage. Jihadist groups such as the Islamic State of Iraq and the Levant — an offshoot of the main Islamist opposition group in Syria, Jabhat al-Nusra — are fewer in number than more moderate forces, but they are considered some of the best-equipped and most effective fighters on the battlefield.

Moderate rebels say they have been left behind militarily as radical Islamist groups receive arms and financial support from elsewhere, while weapons pledged to the moderates by the United States have yet to arrive. Although Jabhat al-Nusra is seen as “more adept at coordinating its efforts on the battlefield with other groups,” a U.S. official in Washington said, “whether the groups will be able to set their differences aside and cooperate against Assad is really an open question.” The official spoke on the condition of anonymity to comment on a still-fluid situation.

“The Islamic State phoned me saying that they killed Abu Bassir and that they will kill all of the Supreme Military Council,” a spokesman for the Free Syrian Army, Qassem Saadeddine, told the Reuters news agency, referring to the FSA executive body.

A look at the Syrian uprising nearly two years later. Thousands of Syrians have died and President Bashar al-Assad remains in power, despite numerous calls by the international community for him to step down.

“We are going to wipe the floor with them,” a rebel commander who spoke on the condition of anonymity told Reuters.

The details of Thursday’s killing were unclear, but the Britain-based Syrian Observatory for Human Rights said that Hamami, one of 30 military leaders on the Supreme Military Council, was shot after an attack on one of the checkpoints he had set up in a mountainous area outside the city of Latakia. Saadeddine said he had been discussing battle plans with members of the Islamic State of Iraq and the Levant.

Despite growing frictions, moderate factions and jihadist groups do still coordinate on the ground, said Charles Lister, an analyst at IHS Jane’s Terrorism and Insurgency Center. He said that is unlikely to change, although the FSA may use the assassination for political gain.

“Moderate forces could use this as a way to prove to the West that they are willing to break relations with jihadis in order to get more Western assistance,” he said. “The reality is very different for the commanders on the ground.”

Louay al-Mokdad, a political and media coordinator for the FSA, said that Hamami was killed by “the forces of evil.”

“We must take the necessary measures, on all levels, and the Islamic State of Iraq and the Levant brigades should hand over to us those who killed Hamami,” he told al-Arabiya television. FSA officials were to hold an emergency meeting Friday to discuss their response, he said.

Mouaz al-Khatib, a moderate Syrian cleric and former head of the Syrian Opposition Coalition, said in a statement that the killing by “a criminal gang that knows no religion. . . and believes jihad to be blood and murder” could be the beginning of a division that would devastate the country.

The stamp of the Islamic State of Iraq and the Levant has appeared on graphic video footage from Syria showing beheadings. The group had not released an official comment on the assassination Friday night. However, a Twitter feed often used to disseminate the group’s views acknowledged the killing, saying: “This man was blaspheming God . . . so God’s ruling was implemented against him.”

While the killing underscores the dissension between the U.S.-backed FSA and Islamist extremists whom the United States and other supporters of the rebels have tried to isolate, it also comes in the wake of discord among the Islamic factions themselves.

The existence of the Islamic State of Iraq and the Levant was first announced in April by Abu Bakr al-Baghdadi, the head of al-Qaeda’s Iraqi affiliate, following the State Department’s designation of Jabhat al-Nusra as an “alias” and terrorist subsidiary of the Iraqi group. While Jabhat al-Nusra “sought to portray itself as part of the legitimate Syrian opposition,” the State Department said, it was merely “an attempt [by al-Qaeda in Iraq] to hijack the struggles of the Syrian people.”

The day after Baghdadi’s announcement, Jabhat al-Nusra’s leader, Abu Mohammed al-
Jawlani, released a video pledging allegiance to the overall al-Qaeda leader, Ayman al-Zawahiri, but denying there had been any merger with Baghdadi’s Iraqi group.

Last month, after reports that the claimed merger had led to battlefield infighting and defections from Jabhat al-Nusra to an Islamic State of Iraq and the Levant splinter group, al-Jazeera published a letter it said came from Zawahiri chastising Baghdadi for claiming a merger under his leadership.

Syria, Zawahiri said, was the “spatial state” for Jabhat al-Nusra under Jawlani, and Baghdadi’s rule would be confined to Iraq.

“It’s reasonable to think that a fair number of ISIL militants are Iraqis” and more beholden to Baghdadi than to leaders inside Syria, the U.S. official said.

DeYoung reported from Washington. Ahmed Ramadan in Beirut contributed to this report.