With Islamic militants at the vanguard of what appears to be a general Sunni uprising against Baghdad’s Shiite-dominated government, the conflicts in Syria and Iraq are beginning to merge under the strains of sectarian and ethnic competition.

The shockwaves are already reverberating in Syria’s civil war and changing the calculus of both the regime of President Bashar al-Assad and the Syrian armed opposition. One element of that opposition is the Islamic State of Iraq and the Levant, also known as ISIL or ISIS. Last week it seized Mosul and it has advanced on Baghdad, raising alarm bells in Washington – and in Damascus, which had previously shown tacit tolerance for a group that controls a swath of northeast Syria.

Over the weekend, the Syrian Air Force staged its first major attacks on ISIS strongholds in the provinces of Raqqa and Hasakeh. These strongholds were the launching pad for the group's recent gains in Iraq. The UK-based Syrian Observatory for Human Rights said that Syrian jets had targeted ISIS headquarters in Raqqa and the group's religious courts. There was no word on casualties.

“ISIL was useful to the [Assad] regime and [Assad’s ally] Iran for the pressure it put on the Syrian opposition,” says Frederic Hof, senior fellow at the Atlantic Council’s Rafik Hariri Center for the Middle East. “But given what's happened in Iraq, ISIL's shelf life in Syria has expired.”

Although sworn enemies on paper, ISIS has largely refrained from fighting the Syrian regime to focus on building an Islamic state in northern Syria and ousting more moderate rebel rivals. In return, the regime has left ISIS alone, allowing the Syrian military to concentrate on fighting the moderate rebel groups. At the same time, Assad also points to the brutal exploits of ISIS and other jihadist groups in the conflict to justify its argument to the international community that it is fighting Islamic “terrorists.”

The Iraq upheaval appears to have changed that calculation. It has also injected uncertainty into Assad's reliance on Iraqi Shiite fighters to seize the upper hand in Syria's war.

In recent weeks, “thousands” of Iraqi Shiite fighters who were in Syria to defend the Assad regime have left, according to a diplomatic report from a European embassy in Beirut. Some of the Iraqi Shiites withdrew from the town of Rankous in the mountainous Qalamoun region north of Damascus. Two months ago, the town fell to the Assad regime. Last week, Syrian rebels took advantage of the weakened regime presence in Rankous to mount a counter-attack in which at least 11 Lebanese Shiite Hezbollah fighters were killed.

“The rebels launched a surprise attack on the edge of Rankous. The fighting is ongoing,” says a veteran Hezbollah combatant who has served multiple tours in Syria.

Challenge of holding territory

Despite a succession of battlefield successes in western Syria over the past year, the Assad regime barely has sufficient forces to hold its newly seized territory. With the Syrian Army weakened by desertions and exhaustion, the regime relies heavily on its allies, chiefly Hezbollah as well as Iraqi paramilitaries and the National Defense Force (NDF), a militia composed mainly of Alawites, the splinter Shiite sect to which Mr. Assad belongs.

It is estimated that there are around 5,000 Hezbollah fighters in Syria at any one time and they have spearheaded key offensives in the past year, backed by Syrian air power and artillery. Before the ISIS offensive in northern Iraq, there were an estimated 20,000 to 30,000 Iraqi Shiite fighters serving in Syria, most of them ill-trained recruits on six-month contracts offered by Iran with a promise of a job upon return. The Iraqi Shiites mainly defend religious sites and man checkpoints. The strength of the Iran-trained NDF is thought to have reached 80,000.

Even before ISIS seized Mosul, some Iraqi Shiites were pulled out of Syria in response to rising tensions in Iraq where Sunni militants had a growing presence in Anbar Province. But the advance toward Baghdad and a vow by Abu Mohammed al-Adnani, the group’s spokesman, to take the war to the “filth-ridden city” of Karbala and Najaf, “the city of polytheism,” both containing paramount Shiite shrines, has upped the ante. For Iraqi Shiites in Syria, protecting these holy sites is a more pressing priority than defending Assad’s regime.

A drawdown of Iraqi Shiites could make Syria's regime even more dependent on Hezbollah fighters, further straining the Lebanese group’s support base. Lebanese Shiites generally have supported Hezbollah’s intervention in Syria, especially when Shiite areas of Lebanon suffered suicide bombings last year by extremist Sunni groups.

But the last car bombing occurred at the end of March, and since then Lebanon has enjoyed a period of relative calm. Now, there is a sense of unhappiness building among the families of Hezbollah fighters. They are increasingly asking how much longer their fathers, husbands, brothers, and sons will be sent to fight and die on the Syrian front.

Regional recalculations

More broadly, the Iraq crisis could change the regional and international calculus toward Syria. The sight of ISIS militants equipped with American vehicles and weaponry looted from Iraqi Army bases may further dampen the White House's willingness to supply arms to moderate Syrian rebels in case they fall into the wrong hands.

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Iran also is having to recalibrate its position in light of the Iraq crisis. Tehran has committed a significant financial and military investment in propping up the Assad regime over the past three years. It also is showing a willingness to come to the rescue of Prime Minister Nouri al-Maliki's government and reportedly has dispatched elite troops to Baghdad.

“Iran’s primary interest has been to maintain the axis of Iran, Maliki’s Iraq, Assad’s Syria, and Hezbollah in Lebanon,” says the European diplomatic report. “Iran is therefore now entering its very own two-front situation [Syria and Iraq] and may face a lengthy problematic situation that could affect the quantity and quality of the financial and military support to Assad’s Syria.”