U.S. strikes against the self-proclaimed Islamic State have had an unintended beneficiary: al Qaeda.

Al Qaeda has exploited the strikes and gained strength, and that has created a growing rift within U.S. national security circles about where the coalition should aim its strikes. Some American intelligence and defense officials and counterterrorism experts are worried that the intense focus on defeating ISIS has blinded the U.S. to the resurgence of al Qaeda, whose growing potency has become more apparent as ISIS becomes weaker.

The American air campaign has notably not targeted al Qaeda in Syria, known as Jabhat al Nusra. With its foe, ISIS, under daily coalition bombardment, al Qaeda has been thriving, continuing to re-align itself with local forces, and re-emerging as the world’s enduring terror group.

“Now, al Nusra Front and [ISIS] don’t get along… I guess you could say to the extent that we’re weakening [ISIS], maybe it benefits al Nusra Front,” Lt. Gen. Sean MacFarland, the top U.S. commander in the war against ISIS, conceded in a recent briefing with reporters.

In recent days, al Qaeda’s standing in Syria has come under attack in the city of Aleppo, that nation’s commercial hub. U.S. officials now are watching Aleppo to see if al Qaeda’s close relationship with local Syrian forces can endure, even when its fighters are forced to flee the front lines.

Opponents of striking al Nusra note the al Qaeda affiliate is one of the few forces that can keep Syria from devolving into a battle between Syrian President Bashar al-Assad and the Islamic State. That is, in Syria, the U.S. is actually worried about the effect of al Qaeda losses.

Supporters of doing more are led by the U.S. military’s Central Command, which oversees American efforts in the Middle East, according to two defense officials.

“There is concern about it because Jabhat al Nusra and al Qaeda are rebuilding,” a senior defense official familiar with the U.S. war against ISIS told The Daily Beast. “The strikes and the chaos of the region have opened the door for them.”

Indeed, al Nusra has even fought alongside local rebel groups that receive weapons and support from the U.S., making al Qaeda’s Syria branch a sometimes indirect beneficiary of American intervention in the conflict. David Petraeus, the influential former general and CIA chief, has even floated the idea of working directly with al Nusra moderates to battle ISIS.

And yet the U.S. declared al Nusra a terrorist organization in late 2012.

“In Syria, it’s actually remarkable that they managed to survive despite ISIS,” Barak Mendelsohn, a professor and terrorism expert at Haverford College and the author of The Al Qaeda Franchise, told The Daily Beast. He attributed al Qaeda’s success in part to the lessons it learned in Iraq, where, a decade ago, a violent branch of the terror group alienated locals through a systematic campaign of terror, beheadings, and the imposition of strict Islamic rule. The remnants of that group went on to become ISIS.

Today, al Nusra isn’t making the same mistakes. “They have put a more friendly face on their actions and are embedding themselves within insurgencies so they’ll be more welcomed by the people,” Mendelsohn said.

Such lessons, and subsequent al Qaeda gains, have reached outside of Syria. From Libya to Yemen to Afghanistan, al Qaeda has managed to dig in and survive, largely by insinuating itself into local populations and rebranding itself as the world’s more reasonable global Islamic jihadist movement. At the same time, ISIS, with its boisterous propaganda, barbaric execution videos, and apocalyptic vision, has captured the most public attention and become the main target of the Obama administration’s fight against extremism.

Al Nusra has sought to portray itself as a credible rebel force fighting with the Syrian people to overthrow al-Assad. That has helped the group win local support and turn people against ISIS, even though both groups want to ultimately establish an Islamic government.

Al Nusra “suffered a string of setbacks in 2014 that forced the group to retrench and rebrand. After those setbacks, [it] was able to parlay the success of battlefield gains against a weakened Assad regime into greater strength and credibility as a ground force,” a U.S. counterterrorism official told The Daily Beast.

“The group’s efforts to cloak themselves as a local force battling the regime, while maintaining the support of the broader al Qaeda network, has helped it emerge as one of al Qaeda’s most potent affiliates,” the official said.

A U.S. intelligence official told The Daily Beast that despite “significant leadership losses” in the past year, “some of [al Qaeda’s] affiliates sought to expand their footprint by taking advantage of local conflicts and perceived grievances.” That model has worked in Syria and in Yemen, where the official said al Qaeda had exploited “increased instability” in the country, gripped by civil war, “to bolster recruitment and gain territory.”

“It’s clear that as [ISIS] loses steam, other Sunni extremist groups like al Qaeda could look to reassert themselves,” the official added.

As al Qaeda aligns itself with local forces, it increasingly finds that onetime Western foes are unwilling to attack them, in Syria and beyond. In Yemen, Saudi Arabia has notably stopped short of launching strikes in the southern part of the country, where al Qaeda dominates the area. And the U.S.-led coalition in Syria has been reluctant to strike al Nusra, allowing the group to switch alliances as needed to survive the war there. In Syria, U.S. airstrikes are largely aimed at ISIS positions in the east, not at al Nusra positions in the country’s north.

U.S. military officials argue that, even if their choice of strikes sites may be benefiting al Qaeda in Syria, it doesn’t matter because al Qaeda will use its renewed strength to go after ISIS.

“If [ISIS] and al Nusra Front want to fight each other, I wish them both success, but, you know, we’re here to defeat [ISIS], and that’s what we’re going after every day,” MacFarland said.

So far, however, that scenario hasn’t happened. Rather, al Qaeda has worked on gaining territory and influence across the region. In the past week, al Qaeda militants in Yemen reclaimed the town of Azzan, a major commercial hub that the group had previously controlled but lost in 2012.

With the U.S. military determined to attack primarily ISIS, the biggest threat al Nusra faces is Russian airstrikes, which target all forces opposed to Assad, including rebel groups backed by the American government. The Institute for the Study of War, which tracks Russian strikes, found (PDF) that most of them hit groups other than ISIS, and often al Nusra.

In Oman on Wednesday, Russian Foreign Minister Sergei Lavrov told reporters, “Russian airstrikes will not cease until we truly defeat the terrorist organisations [ISIS] and Jabhat al Nusra.”

While American forces have occasionally targeted al Qaeda cells in Syria that are looking to attack the West, the U.S. focus remains almost exclusively on ISIS for now.

The fight against the Islamic State is receiving a significant boost in the latest Defense Department budget, which allocates an additional $7.5 billion to fight the group, a 50 percent increase from current funding. An additional $1.8 billion is allocated for more than 45,000 additional GPS-guided smart bombs and laser-guided rockets, commonly used in the air campaign against the Islamic State.

A Pentagon official explained to The Daily Beast that part of those funds are to potentially expand the U.S. effort to attack ISIS in Libya, where its presence is on par with al Qaeda.

For now, as long as ISIS conducts high-profile attacks, like the mass shootings and bombings in Paris and the downing of a Russian airliner, al Qaeda is not the priority. “The problem is everything is about ISIS every day,” the defense official said. “You only have so many rounds in your chamber.”