How Did the United States End Up on the Same Side as the Muslim Brotherhood in Yemen?

Extremism in Yemen has never solely been a Yemeni problem. Terror organizations with global ambitions have long operated from the country. Civil war has drawn in neighbors and regional powers like Iran, Saudi Arabia, and the United Arab Emirates.

It has never been a simple conflict. Just some of those on the battlefield are al-Qaeda in the Arabian Peninsula (AQAP); the Houthis (a terror group from Yemen’s Zaidi Shia minority with Iran’s backing); the Yemeni government, in various forms; and a unique strain of the Muslim Brotherhood (Islah), also a part of the government.

As the Trump administration targets Muslim Brotherhood branches across the Middle East, the branch in Yemen is a strange case, in many ways opposed to American priorities, but also a partner in the fight against other enemies.

Unlike in other countries, the group has never been America’s biggest concern in Yemen, despite it being the country’s main Islamist party. It encompasses a range of the myriad political and tribal segments of Yemeni society and denies being part of the Brotherhood at all, despite the crucial, and ongoing, role of Brotherhood leaders in founding the party and its shared ideology.

Islah has been hugely influential on both the political and military stages in Yemen and has held a significant role in successive U.S.-supported governments. To understand U.S. policy towards Islah requires an understanding of the adversaries and political complexities that have formed modern Yemen.

Al-Qaeda’s Role in Yemen

The first major terror threat the United States confronted in Yemen was al-Qaeda. Cells and operatives of the transnational terror organization have been active in the country since the 1990s, when jihadis returned from fighting in Afghanistan. It was al-Qaeda’s network in Yemen that bombed the USS Cole in the port city of Aden in 2000. Seventeen U.S. servicemembers were killed. In 2009, the group was behind the unsuccessful “Underwear Bomber,” who attempted to detonate an explosive in his pants on a Christmas Day flight from Amsterdam to Detroit. In that same year, AQAP was formed from a merger of the terrorist group’s Yemeni and Saudi branches.

It wasn’t long after AQAP’s formation that U.S. officials considered it to be the most significant al-Qaeda threat to the United States. This concern was due, in no small part, to Ibrahim al-Asiri, AQAP’s skilled bomb-maker who was behind the terror group’s more innovative and alarming plots. America’s program of targeted drone strikes in Yemen, beginning in 2002 and accelerating after 2009, was partially motivated by a sense of urgency to kill Asiri. He was killed by a U.S. strike in 2017.

AQAP largely focused on attacks against the West, but also held territory of its own in Yemen following unrest and insecurity brought on by the Arab Spring in 2011 and territorial advances by the Houthis in 2014. They were uprooted in 2016, but have since reestablished a presence and conducted attacks on Yemenis.

The Houthis Become Major Players

In the 2000s, with al-Qaeda already on the scene, the Houthis emerged as a threat to President Ali Abdullah Saleh’s central government. His inability, or unwillingness, to defeat the Houthi guerilla insurgency from 2004 to 2010 weakened the Yemeni state. In 2014, the group burst southwards from Saada, their home governorate, and expanded rapidly across the country, capturing the nation’s capital, Sanaa, in September and seizing much of western and southern Yemen by the spring of 2015.

In the early years of the war against the Iran-backed Houthis, AQAP — Sunni jihadists ideologically and theologically at odds with the Houthis — fought alongside the government, which included Islah forces. With the United States backing the internationally recognized government (IRG), it found itself on the same side as Islah and AQAP. The Houthi expansion brought another marriage of convenience as former President Saleh, ousted from office in late 2011, entered an opportunistic alliance with the Iran-backed terror group. It lasted only three years before the relationship soured and the Houthis killed him in 2017.

In 2015, Saudi Arabia led a coalition of Arab states, supported by Washington, to fight the Houthis. The coalition pushed the Iran-backed group out of much of the south that year but fighting continued in various fronts in the north. Conflict lines became largely static after a cooling of relations between the United States and Saudi Arabia in 2018, and the UN-brokered a truce in 2022.

Another Year, Another Alignment of Players

Nearly a decade after fighting the Houthis, AQAP adapted again, this time entering an “opportunistic alliance” with the Iran-backed group, according to the 2024 report by the UN Panel of Experts on Yemen. The two terror groups subordinated ideological and religious differences to their shared interest in fighting Israel, the United States, and the West, while promoting instability in Yemen. The alliance may not be as strange as it seems on the surface. Iran hosts al-Qaeda’s current overall leader, Sayf al-Adl.

Elsewhere in Yemen, various factions that agreed on little but their opposition to the Houthis, came together to fight them. In April 2022, Yemeni President Abdrabbuh Mansour Hadi, who had been in office since Saleh’s ouster more than a decade before, transferred power to a new eight-man executive body, the Presidential Leadership Council (PLC), at the request of multiple Arab Gulf states. The members of the PLC represented different factions intended to bridge political, tribal, and other divisions and included two Islah-affiliated members.

These disparate factions included the secessionist Southern Transitional Council (STC), backed by the United Arab Emirates and a rival of Islah. The STC advocates for an independent South Yemen, as existed prior to 1990. Islah, a primarily northern political force supported by Saudi Arabia, opposes splitting Yemen, as do most northern segments of Yemen’s political landscape.

The two organizations’ political differences, which have boiled into open conflict at times, are exacerbated by southern distrust after Islah’s involvement in atrocities in the south during and after the brief 1994 north-south civil war. Further complicating matters, the UAE designated the Muslim Brotherhood as a terrorist group in 2014.

Following the STC’s rapid expansion and then fall in late 2025 and early 2026, the UAE has been ousted from Yemen by Saudi Arabia and resolution of the southern issue is now being spearheaded by Riyadh. The same set of challenging options that the United States faces has now driven a wedge between previously close allies Saudi Arabia and the United Arab Emirates, already on different sides in other arenas.

Islah’s Political Longevity

Although the PLC is Yemen’s first coalition-style executive, it is not Islah’s first time in Yemen’s power center. Islah has been a major player in Yemen’s political scene for three decades and represents a wide constituency including Brotherhood acolytes, Salafis, and tribal factions. General Ali Mohsen al-Ahmar was Islah’s long-time godfather in Yemen’s political and military landscape during successive regimes. Under Saleh, he was a prominent military leader and close advisor, though their relationship was at times tense. He split from Saleh in 2011. He continued in influential military leadership roles under President Hadi’s government and was elevated to vice president in 2016.

Despite Ahmar’s role being replaced by the PLC, the party’s ongoing influence was reflected in the elevation of two Islah leaders to the PLC; Major General Sultan Ali al-Arada, a tribal and military leader who gained prominence through military successes against the Houthis, and Abdullah al-Alimi Bawazeer, a longtime Islah bureaucrat. Thus, under the banner of the anti-Houthi coalition government, the United States finds itself aligned with the Muslim Brotherhood in Yemen and has dealt with them in the same way as other parties in the council.

The Current Dilemma

As the Trump administration targets Muslim Brotherhood branches around the world, Islah may find itself in Washington’s crosshairs. Experts and members of the STC have argued that Islah-affiliated leaders have enabled and maintained relations with the Houthis and al-Qaeda. Even the United States has designated numerous Islah leaders for ties to terror groups, most frequently al-Qaeda. Southern reports also allege that Islah forces not only ignore the supply of weapons to terrorist groups in their territory but have actively participated in this illicit activity.

For its part, Islah officially denies being a Brotherhood branch and anything less than a committed partner in the fight against the Houthis. Designating or sanctioning Islah would complicate its involvement in the anti-Houthi coalition as it would put segments of the government, official armed forces, and tribal affiliates on the wrong side of American policy. This could damage cohesion and effectiveness of the coalition against the Houthis. However, allegations that Islah gives Yemeni terror groups a “back door” in the government should be investigated seriously.

Any action against Islah should be part of countering America’s other adversaries in Yemen. American policy against extremist groups in Yemen has been lacking. In the spring of 2025, after a year and a half of Houthi attacks on commercial ships in the Red Sea and Israel, the United States launched an air campaign against the Iran-backed terror group that included more than 1,000 strikes. That ended in a ceasefire between the two sides in May that has failed to protect commercial shipping or Israel.

Washington must keep the Houthis as the central focus in Yemen. But it can’t afford to forget about the other actors in who pose short-, or long-term, threats to the United States. AQAP is still active in Yemen and, through Islah, the Muslim Brotherhood is playing a role that is unlikely to align with U.S. interests for long.

Bridget Toomey is a research analyst at the Foundation for Defense of Democracies (FDD). For more analysis from Bridget and FDD, please subscribe HERE. Follow Bridget on X @BridgetKToomey. Follow FDD on X @FDD. FDD is a Washington, DC-based, nonpartisan research institute focusing on national security and foreign policy.