In 2006, US-led forces in Iraq managed to locate and kill the top leader of al-Qaida in Iraq (AQI), Abu Musab al-Zarqawi, in what turned out to be a landmark operation.The significance of the targeted killing was not only that the world had one less terrorist on its hands, but moreover, evidence emerged that it probably would not have been so easy to find Zarqawi if not for the fact that other members of al-Qaida had grown weary of his brutal penchant for targeting Shi’a civilians, which was turning Iraqi public opinion against al-Qaida.Over the subsequent two years Western forces managed to hunt down hundreds of AQI fighters leading to the thought that by the end of 2008, thanks to collaboration by numerous local informants, AQI was going extinct.The author is a PhD candidate at Tel Aviv University and research fellow at the Moshe Dayan Center, who specializes on Syria.Many survived, however, and the inheritors of Zarqawi’s organization became the Islamic State of Iraq (ISI).They have revived operations since the outbreak of the so-called Arab Spring in early 2011 and following the US withdrawal from Iraq at the end of that year. Nearly daily bombings in Iraq have been witnessed, which are usually claimed by the ISI Sunni Muslim terrorist organization, and have slaughtered thousands of Shi’a Muslim civilians.In addition, in 2013, ISI grew in strength to become one of the leading rebel forces in Syria, where it is led by Abu Bakr al-Baghdadi and goes by the name Islamic State of Iraq and al-Sham (Greater Syria).The Syrian-based branch, ISIS, unlike its main al-Qaida-linked rival, al-Nusra Front, is mainly comprised of non-Syrians and instead of fighting the Syrian regime of Bashar al-Assad directly, has focused its efforts on taking over areas already controlled by the multitude of rebel factions in the northern and eastern parts of Syria near Iraq and along the Turkish border.In addition to forcing smaller rebel groups to pledge allegiance or face annihilation, ISIS has been engaged in a series of battles with Kurdish militia groups established to defend what have become nearly autonomous areas where the Kurds are a majority in north-eastern Syria. In a video released on the 8th of November by Al-Jazeera, the top leader of al-Qaida, Egyptian-born Ayman al-Zawahiri, has called on the loyal leaders of al-Nusra Front and ISIS to end their rivalry and cooperate solely under the banner of al-Nusra Front.This move is meant to end a rivalry that began early this year when ISIS leader Abu Bakr al-Baghdadi announced that he was the emir, or prince, of all true jihadis and effectively became the pre-ordained head of the “state” he and his organization are planning to establish to enact strict Islamic legal codes over the populations of the Greater Syrian and Iraqi region, which includes Lebanon, Jordan and Israel, as well as Syria and Iraq.In April, 2013, the leader of al-Nusra Front, Abu Muhammad al-Golani, refused to pledge allegiance to al-Baghdadi, since al-Nusra Front had established a relatively large support base among the rebels for their numerous high-level attacks against Assad government targets, which sometimes killed civilians as well.Golani appealed directly to the top al-Qaida leader, Zawahiri, who agreed at that time that the two organizations could remain separate and still receive the blessing of al-Qaida. Analysts have noted that in the process many of the fighters coming from abroad to fight in the jihad against the Assad regime and all unbelievers defected to ISIS, leaving al-Nusra Front with a smaller contingent, mainly from Syria.Zawahiri, it turns out, has had a complex relationship with the predecessor of ISIS since the days of Zarqawi.A split between al-Qaida’s Afghanistan- based leadership and al-Qaida in Iraq came to light through a letter from Zawahiri to Zarqawi, which was intercepted and authenticated by US intelligence in mid-2005.The strongly-worded letter indicated that AQI may eventually lose the war for the hearts and minds of the people due to bloody images of Arab Iraqi civilians, and the destruction of famous Islamic monuments because they happened to be Shi’a Muslim instead of Sunni, like al-Qaida and Saddam Hussein. Zawahiri stressed that he of course was well aware of the evils of the Shi’ite heresies, but nevertheless, since most people are not experts in theology, he advised that it was best to avoid tarnishing the image of al-Qaida and to focus solely on attacking American and Israeli targets.Zarqawi both before and after receiving the letter seems to have ignored the content of Zawahiri’s message and continued to mastermind bloody attacks against Shi’ite targets until his demise.The leader of al-Nusra Front, Abu Muhammad al-Golani, has argued in some of his public statements, in fact, that his organization does not want to repeat the mistakes of the AQI during the mid-2000s, and like Zawahiri, prefers not to target non-combatant minorities in so far as it might tarnish the image of the movement. However, the leader of ISIS, al-Baghdadi, seems to derive his authority from his time as an integral part of AQI, and a loyal follower of Zarqawi.Thus, the ISIS tactics tend to differ from those of al-Nusra Front, and while the ideology might be similar, in practice, the ISIS has been suspected of executing those who do not conform to the strict interpretation of Islam they promote.Moreover, recent reports have emerged through the Syrian Observatory for Human Rights, based in the UK, that ISIS followers have been destroying “idolatrous” cultural monuments in Raqqa – the only provincial capital in Syria that the rebels have managed to hold in the past three years of fighting.While the differences between al-Nusra Front and ISIS may seem small to outside observers, the civilian leaders of the Syrian Opposition are faced with a deep dilemma. Many of the civilian leaders bristled last year when the Obama administration conditioned US support for the opposition on a clear distancing from al-Nusra Front – perceived then as the only serious organization linked to al-Qaida – due to its many high-profile attacks against the Syrian regime in 2012.Military commanders of the rebels on the ground, such as the official head of the Free Syrian Army, Salam Idriss, also argued that the rebels could not win without the brave tactics of the Nusra Front.However, today, with the emergence of the ISIS and its direct links to the highly sectarian AQI and its civilian-targeted violence in Iraq, the already weakened civilian leadership of the Syrian Opposition is faced with an unpleasant choice of becoming even more isolated from movements on the ground or risking what little international support they have by joining with al-Qaeda’s leader in affirming the legitimacy of al-Nusra Front, while trying to distance themselves from ISIS, and its association with Taliban- like social values and unfettered sectarian carnage.