The Obama administration has been caught flat-footed once again—this time in Kyrgyzstan. The administration didn’t anticipate the spring riots escalating and sweeping away corrupt President Kurmanbek Bakiyev and his clan. The U.S. was perceived as being too close to Mr Bakiyev, yet it did not move fast enough to distance itself from him and recognize the temporary government led by Roza Otunbayeva.

While Ms. Otunbayeva—who has served as Kyrgyzstan’s foreign minister three times, as well as its ambassador to Washington and London—is a moderate, she is also close to Moscow. Once in office, she immediately sent her deputy to meetings in the Kremlin. One likely topic at those talks was the future of America’s Manas base—no small annoyance to Russia, which also has a military outpost in Kyrgyzstan.

Russia supported “Roza’s Revolution” despite its past opposition to the 2003 Rose Revolution in Georgia, the 2004 Orange Revolution in Ukraine, and the 2005 revolt in Kyrgyzstan. The reason is likely because Mr. Bakiyev, like the leaders of those other uprisings, was too close to the U.S. and China for Moscow’s comfort.

Mr. Bakiyev’s rampant corruption and nepotism included appointing his young son, Maksim, as head of the nation’s development agency. For a while, the opposition and the media were free to protest Mr. Bakiyev’s regime. But in the last couple of years he has been on a rampage against opposition leaders. Because of the war in Afghanistan, Washington had to hold its nose and deal with Mr. Bakiyev and his predecessor.

In 2007 and 2008, Russia put significant pressure on Kyrgyzstan to kick the U.S. out of the Manas air base, which is crucial to resupplying troops in Afghanistan. Moscow handed Mr. Bakiyev a $2 billion assistance package in credit and loans. In January 2009, however, Mr. Bakiyev signed a deal with the Americans anyway.

This spring Moscow retaliated by hiking tariffs for energy supplies and blasting Mr. Bakiyev on Kremlin-controlled TV channels as a tyrant. In addition to the continuous U.S. military presence, Moscow was also miffed by Mr. Bakiyev’s growing ties with Beijing, which included roads and railway projects.

Immediately following last week’s revolution, Vladimir Putin distanced himself from Mr. Bakiyev and offered help in quelling unrest. That, coupled with the provisional Kyrgyz government’s publicly expressed “gratitude” to Moscow for its “assistance” to the revolution, indicates that there may be deeper Russian involvement than meets the eye.

The main short-term challenge for the Obama administration will be to put distance between itself and Mr. Bakiyev. To that end, the U.S. can offer the provisional government assistance in putting the deposed president on trial for embezzlement and the murder of dozens of demonstrators. As this provisional government in Bishkek is constituted, the State Department and the Pentagon would do well to work closely with it.

The main long-term challenge for the U.S. will be to keep the Manas base open, even if Moscow disapproves and offers an alternative route with a higher level of Russian control. Ms. Otunbayeva already has said that Manas will continue to function “until the current contracts expire”—which will happen this summer.

The White House should provide Ms. Otunbayeva an opportunity to visit the Washington, D.C., which she knows so well, to discuss the future of U.S.-Kyrgyz relations. Manas should remain America’s top priority, but for impoverished Kyrgyzstan, developing small- and medium-sized businesses and fighting corruption are paramount. The State Department should signal that the assistance package for Kyrgyzstan will be generous. The administration need not worry that Ms. Otunbayeva—Kyrgyzstan’s “Ms. Clean”—will inappropriately benefit from U.S. taxpayer help.

In the last couple of years, Russia has scored some points in its “roll-back” of George W. Bush’s Eurasian advances. First, the Georgian war and the European reaction to it all but froze Georgia’s chances for NATO membership. Second, Mr. Yanukovich’s victory in the Ukrainian presidential elections moved Kiev from a pro-Western orientation to neutrality. Now, the U.S. presence in Central Asia, and in Eurasia as a whole, may be at stake.

Cross-posted on The Wall Street Journal op-ed page.