GIVEN THE CIVIL WAR in Libya and serial massacres of opposition demonstrators in Syria , it’s not surprising that another ugly campaign of repression, in the Persian Gulf emirate of Bahrain, hasn’t gotten much attention. In its own way, however, Bahrain could prove crucial to the outcome of this year’s Arab uprisings — and to whether it advances or damages the strategic interests of the United States.

Bahrain is host to the U.S. 5th Fleet, which patrols the Persian Gulf and is vital to the containment of Iran. But the island’s ruling al-Khalifa family, which has long been closely allied with the United States, is ignoring the objections of the Obama administration by systematically persecuting those who joined a pro-democracy movement earlier this year. Since the crackdown began March 14 more than 800 people have been arrested, mostly from the majority Shiite community; many have been tortured and four have died in custody. More than 1,000 people have been fired from their jobs in a country of 700,000. Government employeees are being pressured to sign oaths of loyalty to the Sunni regime.

On Sunday authorities began a trial for 21 leading activists accused of plotting to overthrow the government. The unlikely conspirators range from the leader of Bahrain’s most militant Shiite organization, who returned from exile in London during the protests, to the head of a secular and liberal Sunni party, whose headquarters were recently burned down. Others hauled before the court include prominent human rights activists, Shiite clerics and bloggers. The accused have not been allowed contact with their lawyers and were granted a single phone call with their families. Most say they have been tortured and some have been seriously injured.

The regime’s crude political strategy is to claim that its opposition is inspired and controlled by Iran — though there is no evidence that Tehran had anything to do with the mass protests or their secular, pro-democracy agenda. Those on trial are accused, implausibly, of having ties to “a terrorist organization abroad working for a foreign country.” In the end, Iran is likely to be the beneficiary of the repression, which has had the effect of polarizing the country along sectarian lines and eliminating proponents of moderate political reform.

The Obama administration encouraged the reform route, which was briefly pursued by the regime’s most liberal member, Crown Prince Salman bin Hamad al-Khalifa. But since Saudi Arabia sent troops to the island on March 14,the regime has practiced unrelenting sectarian repression, with Riyadh’s backing. Reluctant to criticize massacres even by U.S. adversary Syria, the administration has been especially circumspect about Bahrain. Its mild message, reiterated last week by the State Department, is that “there is no security solution to resolve the challenges Bahrain faces.”

The administration clearly is trying to protect the strategic relationship with Bahrain. But by tolerating the repression it is endangering long-term U.S. interests, since the crackdown is likely to boomerang, sooner or later, against both the Bahraini and Saudi ruling families. The best way to protect American interests is to tell both regimes that a continued security relationship with the United States depends on an end to policies of sectarian repression and on the implementation of moderate reforms. Meanwhile, it’s time to start looking for a new home for the 5th Fleet.