House Speaker John Boehner said on Wednesday that he was “disappointed” in a Supreme Court ruling striking down the Defense of Marriage Act (DOMA).

The ruling means that federal agencies must recognize the legal marriages of gay and lesbian couples.

“While I am obviously disappointed in the ruling, it is always critical that we protect our system of checks and balances,” Boehner told reporters. “A robust national debate over marriage will continue in the public square, and it is my hope that states will define marriage as the union between one man and one woman.”

After the Obama administration decided it would no longer defend the law in court, Boehner spent millions defending it in more than a dozen separate challenges, some of which will continue.

Other congressional Republican leaders echoed Boehner's sentiments, saying that the fight had shifted to the states.

House Majority Leader Eric Cantor said that “the marriage debate will continue in the states.”

And Texas Senator John Cornyn added: “It sounds to me that that battle will be moving to the states.”

Those sentiments had many wondering whether the GOP, which has previously used the issue to gin up its base, was waving the white flag.