While the Obama administration’s burgeoning contacts with the Muslim Brotherhood in Egypt continue to cause controversy, the administration’s policy of growing cooperation with the Syrian opposition continues to enjoy almost unanimous support. This is remarkable, since by virtue of that policy the administration is openly allied with none other than the Muslim Brotherhood: that is, openly, but with perhaps just enough misdirection for the alliance to escape the notice of the broader public.

The Syrian opposition organization that the United States and other Western powers have been officially supporting is, of course, the Syrian National Council (SNC). At a meeting in Istanbul on April 1, the so-called Friends of Syria, including the United States, recognized the SNC as “a legitimate representative of all Syrians.” Although the use of the indefinite article suggests there were reservations on the part of some participants, U.S. State Department statements both before and after the Istanbul meeting leave no doubt that the Obama administration treats the SNC as its principal Syrian interlocutor. The SNC is also the presumptive recipient or at least conduit of the aid that the Obama administration has pledged to the Syrian opposition. While in Istanbul, Secretary of State Hillary Clinton met with representatives of the SNC, and she afterwards promised that “there will be more assistance of all kinds for the Syrian National Council.”

But who is the Syrian National Council? Although the chairman and most recognizable face of the council is the secular Paris-based political scientist Burhan Ghalioun, it is openly acknowledged that the Syrian Muslim Brotherhood is a major force within the council. In fact, there is strong evidence that it is the major force. When several members of the council resigned in mid-March, they cited the overwhelming influence of the Brotherhood as a reason for their decision. “The Brotherhood took the whole council,” departing council member Walid al-Bunni told the New York Times. “We became like extras.”

The Belgian Syria expert Thomas Pierret, a lecturer in contemporary Islam at the University of Edinburgh, estimates that “around half” of the SNC’s members are Islamists. According to Pierret, moreover, the Muslim Brotherhood controls the council’s “commission on humanitarian aid” and thereby the distribution of SNC funds in Syria. As a consequence of the repression of the organization by the Syrian regime, the leadership of the Syrian Muslim Brotherhood has been living in exile for decades. Pierret notes that the Brotherhood now stands accused of using its control over the SNC aid spigot in order to reconstruct a base of popular support within the country. Pierret cites remarks made by Kamal al-Labwani to the Arab press as the source for the accusation. Al-Labwani is one of the SNC members that resigned in March.

The evidence of Brotherhood dominance of the SNC leads one to wonder whether its secular chairman, Ghalioun, is merely a figurehead. In mid-March, a video emerged of Ali Sadr al-Din Bayanouni, one of the Syrian Muslim Brotherhood’s most prominent members, suggesting precisely this. In the video, Bayanouni claims that the Brotherhood itself had chosen Ghalioun to serve as SNC chair, in an effort to give the council an “acceptable face” vis à vis the West. (The video is available with English and French sub-titles here.) Bayanouni was for many years the head of the Syrian chapter of the Brotherhood. He was succeeded by the organization’s current leader, Mohammed Riad al- Shaqfa, in 2010.

E-mails that were allegedly stolen by pro-regime hackers from an e- mail account owned by Ghalioun appear to confirm that the Brotherhood views its relationship to the SNC chairman much as Bayanouni described it. The e-mails were recently published by the Lebanese newspaper Al-Akhbar. (For a selection of the e-mails in English, see here and here from Al-Akhbar English.) In one of the messages, the Brotherhood’s leading representative on the council, Mohammed Farouk Tayfour, imperiously directs Ghalioun to stop SNC member, Bassma Kodmani, from speaking on behalf of the council. Tayfour is the deputy head of the Syrian Muslim Brotherhood. It should be noted, however, that the Western-educated Kodmani continues to be cited in media reports as an SNC spokesperson — a fact that suggests that there are limits to the Brotherhood’s power in the SNC.

The contrast between the controversy surrounding the Obama administration’s outreach to the Egyptian Muslim Brotherhood and the widespread indifference to its alliance with the Syrian Muslim Brotherhood is particularly odd in light of al-Labwani’s accusation regarding the latter’s control of SNC aid money. For, if this accusation is correct, American and other international support for the SNC does not only imply joining forces with the Muslim Brotherhood: It implies helping the Brotherhood to obtain an influence inside Syria that it did not previously have.