Bahrain, Saudi Arabia and the United Arab Emirates said on Wednesday they were withdrawing their ambassadors from nearby Qatar in what was the first public admission of major differences between the Gulf Cooperation Council states.

In a statement, the three monarchies said Qatar had failed to honor an agreement not to interfere in the affairs of its neighbors. But the real reason for the diplomatic pullout seems to be Qatar’s support for the Muslim Brotherhood, an organization that Saudi Arabia and its allies abhor.

Since the beginning of the “Arab Spring” uprisings in late 2010, Qatar has supported Islamist revolutionary causes in Egypt and Syria and provided hundreds of millions of dollars in aid to the Muslim Brotherhood’s Palestinian affiliate, Hamas. It also hosts the movement’s spiritual leader, Yusuf al-Qaradawi.

Saudi Arabia’s own puritanical strain of Islam, Wahhabism, is at odds with the Muslim Brotherhood’s advocacy of political Islam. The organization also favors republicanism and is populist, unlike Saudi Arabia, a monarchy and authoritarian.

Qatar’s support for the Muslim Brotherhood in Egypt suffered a blow last July when President Mohamed Morsi was deposed by the army. Saudi Arabia and the United Arab Emirates rushed in with billions of dollars in aid for the interim government that succeeded his.

Around that time, Saudi Arabia also assumed a leadership role in coordinating Arab support for the uprising against Syria’s president, Bashar al-Assad. Whereas Saudi Arabia had concentrated its efforts in the south of the country, near the border with Jordan, and allowed a Qatari sphere of influence in the north, near Turkey, the growing prominence of the Muslim Brotherhood in the opposition worried the kingdom which preferred to back less political Salafist.

Both Arab states have sectarian and strategic imperatives for supporting the Syrian uprising. Because Assad is the only Arab ally of their nemesis Iran, replacing his government with a majority Sunni regime would weaken the Shia axis in the Middle East and limit Iran’s retaliatory options in case there is an American or Israeli attack on its nuclear sites which Arab and Western nations suspect are part of a weapons program.

Despite reluctance on the part of Saudi Arabia’s ally the United States, which worries that religious fanatics in Syria might be no better than Assad, the kingdom has stepped up its support for more radical insurgents

The rift between Qatar and the other oil-producing states in the Persian Gulf further calls into question regional integration schemes which have made little progress in recent years.

The alliance, which also includes Kuwait and Oman, failed to agree to plans for a joint missile defense system, despite American support. A Saudi proposal for deeper economic and political union stalled in 2012. Earlier, the United Arab Emirates had pulled out of a planned monetary union.