The Obama administration’s muscular counter-terrorism campaign against a dangerous Al Qaeda affiliate in Yemen is facing a new threat from the sudden military gains and growing political influence of a Shiite Muslim rebel group backed by Iran, according to U.S. officials.

The Houthi rebels seized control of Sana, the Yemeni capital, last month and forced the country’s president, Abdu Rabu Mansour Hadi, to sign a deal giving them a leading voice in the formation of a new government.

The Houthis long have demanded a halt to Yemeni cooperation with U.S. counter-terrorism operations, including drone strikes. If the group maintains its grip on power, they presumably “would want to see that cooperation certainly sharply reduced, if not eliminated,” a senior State Department official said.

Halting the drone strikes would appear contrary to Houthi interests, since the chief U.S. target, Al Qaeda in the Arabian Peninsula, or AQAP, is the Houthis’ archenemy. The two groups have clashed repeatedly in recent days, including an AQAP attack on a Houthi-controlled hospital Sept. 28 that killed 15 people.


Yet the new era of multi-sided Middle Eastern conflicts has brought “the death of the idea that the enemy of my enemy is my friend,” said the State Department official, who asked for anonymity to discuss internal assessments. “It seems not to work that way anymore.”

Rep. Adam B. Schiff (D-Burbank), a member of the House Intelligence Committee, said in an interview that he worries that the crisis in Yemen might lead to a government collapse that “could only enhance AQAP’s ability to control ground and launch terror attacks.”

AQAP is the most dangerous of Al Qaeda’s spinoffs, U.S. officials say, with a history of trying to blow up American airliners.

U.S. officials said AQAP also has provided bomb-making assistance to the Khorasan Group, a supposedly elite Al Qaeda unit in Syria that the White House late last month said posed an imminent threat to the United States and Europe. American warships and bombers have attacked alleged Khorasan positions in Syria in the last two weeks.


The Pentagon and the CIA, with assistance from Yemeni authorities, have used armed drones and special operations raids to kill hundreds of AQAP militants over the last 12 years. So far this year, U.S. forces have launched 19 such airstrikes, killing or injuring 104 fighters and six civilians, according to the Long War Journal, a private website that tries to track the conflict.

In August, President Obama cited the U.S. counter-terrorism operations in Yemen and Somalia to describe the calibrated approach he would take — using American airstrikes and local ground troops — against Islamic State militants in Iraq. The administration and its allies have employed far greater force in Iraq, however, launching more than 250 airstrikes so far.

Houthi fighters took control of Sana on Sept. 21, brushing aside weak Yemeni army forces. President Hadi has been trying to organize a transitional government under a plan negotiated with support from the U.S., United Nations and the Sunni Muslim states of the Persian Gulf region.

But the Houthis forced Hadi to sign a separate deal that ousted the last prime minister and appointed ministers acceptable to them. The group has installed “popular committees” in police stations and key government ministries, and demanded that 20,000 of their members be recruited into the army.


The power grab by the Houthis, who are based in northwestern Yemen, has jolted an unstable but strategically important corner of the Middle East.

Sectarian tension in Yemen has not been nearly as high historically as in other Middle Eastern countries. Some experts say that the conflict in Yemen — an impoverished, crowded country with little oil or water — remains largely a local power struggle.

But U.S. and Yemeni officials, as well as outside experts, worry that friction between the country’s Shiite and Sunni Muslims is worsening, partly because militants see an advantage in casting the power struggle as a religious war.

That may appeal to Al Qaeda because “it can be a recruiting tool,” said Leslie Campbell, who directs Middle East programs at the National Democratic Institute for International Affairs, a nonpartisan and nongovernmental organization that promotes democracy around the globe.


There are also signs that Yemen may become a more important battleground in the competition between Saudi Arabia, which sees itself as a champion of Sunni interests, and Iran, which supports Shiite fighters. Both countries appear to be maneuvering for influence.

Prince Saud al Faisal, the Saudi foreign minister, has been trying to round up allied support, warning late last month of “accelerating and extremely dangerous conditions” in Yemen.

The Saudis, who share a porous 850-mile border with Yemen, fear that Iran will seek to use the Houthis as a destabilizing force, as it has used its ally Hezbollah, a Shiite militia, to project power in Lebanon.

Yemeni officials say they captured, then released, members of the Iranian Revolutionary Guard Corps and Hezbollah who had come to train Houthis. And the senior State Department official said the Iranian government previously has provided arms and possibly money to the Houthis.


“The influence of Iran on the Houthis is absolutely there,” he said.

Iran denies any role in the conflict.

Special correspondent Zaid Al-Alaya’a in Sana, Yemen, contributed to this report.