For years, scores of Islamists who are dissidents, militants and influential clerics from across the Arab world have been living in Qatar. On many occasions, other Gulf Cooperation Council (GCC) states, which would never permit such figures to freely reside on their soil, have expressed frustration with Doha for giving Muslim Brotherhood members and other Islamists a base for their activism within the Gulf. GCC pressure on Qatar to abandon its support for the Muslim Brotherhood came to a climax in March 2014 when Bahrain, Saudi Arabia and the United Arab Emirates (UAE) withdrew their ambassadors to Doha for eight months. Qatar still maintains its ties with Islamist actors throughout the region and still permits Muslim Brotherhood-affiliated clerics such as Yusuf al-Qaradawi to reside in Doha, yet since that diplomatic spat erupted nearly three years ago the Arab Gulf emirate has toned down its support for the Muslim Brotherhood to assuage other GCC states’ security concerns.

Nonetheless, Donald Trump’s presidency may create new challenges for Qatar. Based on Trump's calling the Muslim Brotherhood “radical” and his Cabinet picks, the new administration will likely target the Muslim Brotherhood as the United States pushes to “unite the civilized world against radical Islamic terrorism,” as the president put it in his inaugural address. In Rex Tillerson’s Senate confirmation hearings, the former Exxon Mobil CEO listed the Muslim Brotherhood and al-Qaeda as two security threats for Washington to counter along with the Islamic State (IS). Trump’s pick for director of the CIA, Mike Pompeo, co-sponsored legislation as a congressman to ban the Muslim Brotherhood. Earlier this month, Republican lawmakers re-introduced a bill calling on the US State Department to designate the Muslim Brotherhood as a terrorist organization. Even if the bill fails to pass, there’s reason to expect the State Department under Tillerson to go after the Muslim Brotherhood anyway.

Qatar’s support for groups such as Hamas has created friction in Washington-Doha relations. In 2009, then-Senator John Kerry said, “Qatar can’t continue to be an American ally on Monday that sends money to Hamas on Tuesday.” Yet the emirate’s links to such nonstate actors have, thus far, never caused the United States to punish Qatar in any serious way beyond rhetorical condemnations, criticisms and calls on Doha to clamp down on its citizens who finance terrorism.

Since the United States and Qatar became key military allies in the early 1990s, all US administrations have valued Washington’s close relationship with Qatar, which hosts the forward headquarters of US Central Command at Al Udeid Air Base and is a major trade and investment partner of America. Both in Afghanistan and Iraq, the United States relied on the emirate as a hub for military operations. The United States has accommodated Qatar as a vital Middle Eastern ally even when officials in Washington have been on the opposite side of regional issues from their counterparts in Doha.