Washington has been relying on the Kurdish YPG militia to provide on-the-ground muscle for its campaign against the jihadists, much to the outrage of its NATO partner Ankara.
Turkey regards the YPG -- the armed wing of Syria's PYD Kurdish party -- as little more than an arm of the PKK, and the PKK as a "terrorist" movement waging a separatist war inside Turkey.
President Recep Tayyip Erdogan's government has made it clear that Turkey's seizure of the border town of Jarabulus was as much to halt a YPG advance as it was to deny ground to the IS "caliphate."
Bloody clashes have already broken out between US-backed Kurdish fighters and Turkish-backed forces on the ground in northern Syria, and Washington has been left scrambling for a clear response.
Earlier this month, US officials had praised the YPG-dominated "Syrian Democratic Forces" for their liberation of the IS-held town of Manbij on the western side of the Euphrates.
Then last week, on a visit to Turkey, Vice President Joe Biden said the YPG would "under no circumstances" get US support unless they honored what he said was a pledge to retreat east of the river.
The Pentagon has now suggested that Kurdish fighters have largely obeyed the request to withdraw, but fighting has nevertheless erupted west of the river, drawing anger from Washington.
President Barack Obama's envoy to the coalition against the Islamic State group, Brett McGurk, tweeted a Pentagon statement dubbing the Turkish-Kurdish clashes "unacceptable and a source of deep concern."
For some observers, the confused message from Washington has put at risk a golden opportunity to capitalize on a new willingness by Turkey to finally take the fight to the IS extremists.
Defeat from jaws of victory
"The US is risking grabbing defeat from the jaws of victory," said Matt Bryza, a former member of president George W. Bush's National Security Council and now a fellow at the Atlantic Council.
Obama is due to meet Erdogan on Sunday in China on the sidelines of the G20 summit, his adviser Ben Rhodes said, to discuss "the counter-ISIL campaign and the fact that we need to stay united."
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Bryza and others argue that the United States has been urging Turkey to take a stronger stance against the IS for two years and would be foolish to offend Erdogan now by sticking by the Kurds.
"The president should come out and say what the policy is, because you've got that McGurk versus Biden dissonance," he told AFP.
"What that policy ought to be, I think, is that the United States will work with Turkey to make sure that the YPG goes back east of the Euphrates," he continued.
But not everyone in Washington lays the blames the US side for the new tension -- some point to the Erdogan government's ambivalence in the fight against Islamist extremism and anti-American tone.
"The YPG was not America's first choice as a partner and ally in combating ISIS on the ground, it was really all we were left with," said John Hannah, who advised former vice president Dick Cheney.
Hannah, now at the Federation for Defense of Democracies think tank, is co-author of a report released Monday warning the US may have to relocate military bases outside Turkey if ties worsen.
He argued that if major NATO power Turkey had supported the US-led coalition against the IS group more strongly from the outset, Washington would not have been forced to turn to its Kurdish foes.
"If this turns now into a massive fight between the Turkish army or Turkish-backed forces and the YPG without any understanding that Turkey is going to step in and assume a much larger role against ISIS, it's obviously going to be cause of real new tensions between the United States and Turkey," he warned.
But, whatever Washington and Ankara's disagreements in the past, the latter's new determination to play a more forceful role could be a sign of hope for a broader political settlement in Syria.
Kemal Kirisci, director of the Turkey Project at the Brookings Institution, said Turkey appears to have abandoned its dream of a total Sunni Arab Islamist victory in Syria's civil war.
That, along with Erdogan's partial rapprochement with Russia and Iran, could provide an opportunity for a settlement that could end the bloodshed and should not be hostage to Turkish-Kurdish enmity.
"What's happening here, whether we like it or not, is that Turkey is standing up for what it sees as its national interests, which awkwardly overlap and conflict with the ones the US has," Kirisci said.
"Every player there is trying to muddle through, but there is another level of game that I think is trying to unfold and possibly lead the way to a possible resolution of the conflict."