Saudi Arabia and the United States are now working closely together to bolster Syrian rebels seeking the overthrow of President Bashar al-Assad, reviving in the process an earlier model of covert military cooperation from the 1980s that successfully drove the Soviet Union out of Afghanistan. This time their target is Russia’s last remaining Middle East Arab ally—the Assad regime, whose armed forces are equipped entirely with Russian weapons.

So far, the Obama administration has ruled out providing surface-to-air missiles to the Syrian rebels. But the Saudis are now reported to be going ahead with their own purchase of other non-U.S.-made missiles, apparently with American blessings, as Washington had previously stopped it.

Secretary of State John Kerry held talks with his Saudi counterpart, Prince Saud al-Faisal, in Jeddah on June 25 to discuss the coordination of U.S. and Saudi arms shipments to the Syrian rebels. "We want to make sure that that's being done in the most effective way possible," Kerry said.

The Obama administration’s June 13 decision to provide weapons to the rebels aligns the United States with its two closest allies in the Persian Gulf, Saudi Arabia and Qatar, which have been arming them for over a year now and pressuring a reluctant Washington to follow suit. But the decision also plunges Washington into entangling intra-Sunni Arab disputes, including between these two Arab monarchies, over which Syrian faction should rule in a post-Assad era.

King Abdullah has put Prince Bandar bin Sultan, once the long-serving Saudi ambassador to Washington, in charge of implementing U.S.-Saudi military cooperation in Syria. Regarded as a leading “hawk” in the ruling al-Saud family, Bandar is presently head of the Saudi General Intelligence Directorate, which coordinated Saudi money and arms sent to anti-Soviet “freedom fighters” in Afghanistan, Angola and Nicaragua. Another former Saudi envoy to the United States, Prince Turki al-Faisal, led the covert Saudi arms program in Afghanistan.

One little-publicized consequence of the U.S.-Saudi alliance will be to curb the growing influence of the Muslim Brotherhood in Syria, a key Saudi goal. This has put the Saudi kingdom at direct odds with its neighbor, Qatar, the Islamic group’s prime Arab protector and promoter.

It has also placed the United States in the awkward position of taking sides between its closest Gulf allies. Qatar hosts the Pentagon’s main forward operations center, while Saudi Arabia is the keystone of U.S. efforts to build an Arab military counterweight to Iran in the Persian Gulf.

In this case, the Obama administration has decided to side with the Saudis to prevent extremist Islamic groups like Jabhat al-Nusra, an Al Qaeda branch, from dominating a post-Assad government. In return, the Saudi government has agreed to halt its own arms purchases for fundamentalist Salafi groups it favors elsewhere in the Arab world because of its adherence to this same trend of Islam. Instead, according to Syrian and diplomatic sources in the Gulf, it will join the United States in funneling arms through the U.S.-backed Supreme Military Council, made up of secular rebel fighting groups.

The U.S.-Saudi alliance against the Russian-backed al-Assad regime revives their earlier one in Afghanistan during the Cold War. There, the two collaborated closely in sending billions of dollars in arms to militant Afghan Islamic “holy warriors” fighting to end the Soviet Union’s occupation. U.S.-Saudi aid began with small arms and escalated to the provision of U.S.-made Stinger antiaircraft missiles that were credited with turning the tide of war against Soviet forces.

One major difference between Afghanistan and Syria is it that the two old allies this time have agreed to work against the emergence of an Islamic-dominated government in place of the al-Assad regime. Saudi Arabia backed the rise of the Taliban in Afghanistan and was one of only three countries that ever recognized the Taliban government there. But after many Saudi Afghan veterans joined Al Qaeda in its campaign to overthrow the monarchy, it has become extremely wary of a similar blowback from aiding militant Islamists in Syria.

As during the Afghan war, the opposition in Syria is badly fragmented and the most extremist Islamic ones, particularly Jabhat al-Nusra, have proven the best fighters. Fear of U.S. arms ending up in the hands of Islamic extremists has been a prime factor in the Obama administration’s dithering for months over sending any arms to the rebels.

Another factor, however, has been the Saudi-Qatari tug-of-war over the Brotherhood’s role within the fractious Syrian opposition, also a central cause of the rebels’ inability to agree on leaders for its National Coalition of Revolutionary and Opposition Forces or a government-in-exile to facilitate international support.

The Saudi-Qatari conflict is rooted in the two countries’ radically different experiences with the Brotherhood as well their markedly different reactions to the 2011 prodemocracy uprisings across the Arab world. Qatar enthusiastically embraced the changes that catapulted the Brethren to power in Egypt and Tunisia. On the other hand, Saudi Arabia, after initially helping to orchestrate the overthrow of Muammar Qaddafi in Libya, has come to view the Brotherhood’s rise with growing foreboding.

The Saudis harbor a strong aversion to the Brethren because of what they regard as their unpardonable betrayal of the kingdom after it harbored thousands of them for decades from persecution by secular Arab dictators, first in Egypt and then in Syria.

The Brotherhood, founded in Egypt in 1928 by Hassan al-Banna, is the Arab world’s oldest and best-organized political movement. It fell on hard times after it attempted in 1954 to assassinate Egypt’s military leader Gamal Abdel Nasser, who then jailed or drove into exile thousands of its followers. Most found refuge in the Saudi kingdom, and one Brotherhood leader, Mamoun al-Hodeiby, even became an adviser to the late Saudi interior minister, Prince Nayef.

Saudi Arabia took in thousands more Brethren from Syria in the early 1980s after they attempted to rise up against the late president Hafez al-Assad, father of the current Syrian leader. Between ten thousand and twenty thousand Brotherhood followers were massacred in the Syrian city of Hama in 1982.

Despite Saudi hospitality, the Brotherhood took the side of Saddam Hussein in his invasion of Kuwait in 1990 opposed by a U.S.- and Saudi-led coalition that drove Iraqi forces out the following year. After the war, Prince Nayef proclaimed the group had done “great damage” to the kingdom. “All our problems come from the Muslim Brotherhood,” he said, bemoaning the Saudi decision to offer it sanctuary.

Since the First Gulf War, the Saudis and Brotherhood have repeatedly found themselves on opposite sides. For example, the Brethren opposed the Saudi-initiated Arab Peace Plan of 2002, which offered the normalization of relations with Israel in return from its withdrawal for occupied Palestinian territories. The Brotherhood also supports the radical Palestinian Hamas faction, which belongs to the movement and opposes recognition of Israel.

Even so, when the Brotherhood’s party in Egypt won elections after President Hosni Mubarak’s fall in 2011, the Saudis first sought to turn the page in their bitter history, offering nearly $4 billion in financial and economic aid to the new government. They quickly put $1.5 billion in the Central Bank to help Egypt deal with rapidly falling foreign reserves, but the rest is still pending agreement on specific development projects.

By contrast, the Qataris have now poured $8 billion into Egyptian coffers to help the Brotherhood-led government cope with huge budget of foreign-reserve deficits. The then emir of Qatar, Sheik Hamad bin Khalifa al-Thani, last October became the first Arab leader to visit the isolated Gaza Strip to show his support for Hamas, and he has allowed the group’s officials fleeing Damascus to make Doha an alternative base of operations.

The Saudi-Qatari conflict has opened a wider political fissure among the six Sunni monarchies making up the Saudi-led Gulf Cooperation Council—Saudi Arabia, the United Arab Emirates, Bahrain, Kuwait, Qatar and Oman. This body is supposed to coordinate a common strategy toward Iran and the Syrian rebels. But both Saudi Arabia and the Emirates have become increasingly hostile toward the Brotherhood—the Emirates currently have forty-three Brotherhood members on trial for allegedly plotting to overthrow the monarchy there—while Qatar remains its primary Arab backer.

However, recent battlefield gains by the besieged al-Assad regime have had an electrifying effect on both Qatar and Saudi Arabia. The prospect of Assad surviving has heightened their shared fears of seeing a victory not only for him, but also for Shiite Iran. As a result, according to Syrian rebel and U.S. diplomatic sources, Qatar has also agreed to funnel its arms for the rebels through the secular Supreme Military Council.

The reported Saudi-Qatari agreement on arms shipments, however, has not extended to their equally contentious difference over the Brotherhood’s role in the rebels’ political leadership. In March, the emergence of American-educated Ghassan Hitto as “prime minister” of a government-in-exile provoked yet another confrontation because he is regarded as a Brotherhood, and Qatari, protégé. So, too, is Mustafa al-Sabbagh, the coalition’s current secretary general, even though he lives in Jeddah, Saudi Arabia.

The clash between Qatari- and Saudi-backed factions paralyzed a heated, eight-day meeting held in late May in Istanbul, once again over the choice of leaders. The former sought to block the addition of twenty new members to the National Coalition’s council, a bloc backed by Saudi Arabia and led by Michel Kilo, a Syrian Christian. In the end, the council was expanded by 43 to a total of 114 members. But there is still no agreement on a president, and the fate of the rebels’ government-in-exile remains hostage to the Qatari-Saudi feud.

David B. Ottaway is a senior scholar at the Woodrow Wilson International Center for Scholars and a former Washington Post Middle East correspondent.