Most of the weapons that are smuggled into Syria by Qatar and Saudi Arabia end up in the hands of extremists, reports The New York Times. “The opposition groups that are receiving the most of the lethal aid are exactly the ones we don’t want to have it,” said one American official quoted by the newspaper.

The United States have committed to providing “nonlethal aid” to the Syrian opposition but also support their Arab Gulf allies in their effort to topple President Bashar al-Assad.

Qatar and Saudi Arabia are both majority Sunni states with a sectarian and strategic interest in hastening Assad’s demise. The rebellion against his dictatorship is largely composed of Sunni Muslims and he is Iran’s only Arab ally. The Gulf Cooperation Council states, led by Saudi Arabia, are engaged in a struggle for regional hegemony with Iran. Replacing Assad’s government with a Sunni regime would weaken the Shia axis in the Middle East and inhibit 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.

The two most powerful monarchies in the region are not necessarily backing the same opposition groups in Syria. Qatar appears to be largely supporting the Muslim Brotherhood, an Islamist group that the Saudis want nothing to do with.

Saudi Arabia’s puritanical strain of Islam, Wahhabism, and the largely apolitical Salafist movement are at odds with the Brotherhood’s advocacy of political Islam or Islamism. The organization also favors republicanism and employs populist tactics to gather support in democratic systems. Both pose a challenge to the Saudi monarchial and authoritarian form of government. Policymakers in Riyadh fear that a Muslim Brotherhood that is emboldened regionwide, with leaders in Egypt and Syria, would eventually turn on them.

The arming of radical Islamist elements in Syria coincides with an influx of foreign jihadists and is likely to exacerbate the fault lines between Syria’s majority Sunni population and Alawites, Christians and Druze who have stood warily on the sidelines of the revolt for months, fearing that an Islamist takeover will inhibit their religious freedoms and privileges.

It also calls into question, as The New York Times points out, Republican presidential candidate Mitt Romney’s criticism of the Obama Administration’s reluctance to prop up the Syrian opposition.

In a speech in Lexington, Virginia last week, Romney said that he would ensure that rebel groups who share American values “obtain the arms they need to defeat Assad’s tanks, helicopters and fighter jets.” He stopped short of arguing that the United States should provide such weapons directly though.