Last month, when President Obama finally endorsed gay marriage after years of equivocation, he emphasized that he still thinks states should be free to address the issue as they see fit. Since many voters strongly oppose gay marriage, it is clear why Obama advocates a federalist approach to the question. But it is not clear that he logically can.

Obama’s inconsistency is illustrated by two cases involving gay marriage that the Supreme Court could hear during its next term. Two weeks ago, the U.S. Court of Appeals for the 1st Circuit overturned a law that prohibits federal recognition of state-licensed gay marriages, and last week the U.S. Court of Appeals for the 9th Circuit declined to reconsider a case in which it ruled against California’s ban on gay marriage.

The 1st Circuit case involves Section 3 of the Defense of Marriage Act (DOMA), which the Obama administration stopped defending last year after concluding it is unconstitutional. During the same May 9 ABC News interview in which he declared that “same-sex couples should be able to get married,” Obama said DOMA “tried to federalize what has historically been state law.”

But Obama does not argue that DOMA violates the 10th Amendment by impermissibly intruding on a power that the Constitution reserves to the states. Instead, he says the law violates the guarantee of equal protection implicit in the Fifth Amendment’s Due Process Clause.

As Attorney General Eric Holder explained in a February 2011 letter, “The President and I have concluded that classifications based on sexual orientation warrant heightened scrutiny” under the Due Process Clause and that DOMA’s distinction between heterosexual and homosexual couples fails that test. If so, it is hard to see how the same distinction at the state level could pass muster under the 14th Amendment, which says “no state shall … deny to any person within its jurisdiction the equal protection of the laws.”

“If you believe the matter should be left to the states,” Stanford law professor Michael McConnell recently told The Washington Post, “that means you think the Constitution permits the states to take a different view. I don’t see how that can be squared with Attorney General Holder’s claim.”

In fact, Holder and Obama implicitly have staked out a stronger position against state bans on gay marriage than the 9th Circuit did. Under the heightened scrutiny favored by Obama, the government must show that a legal distinction based on sexual orientation is “substantially related to an important government objective.”

The 9th Circuit, by contrast, applied the “rational basis” test, the standard typically used in equal protection cases that do not involve a fundamental right or a “suspect class” such as race. Under that standard, the government need only show that the challenged law “bears a rational relation to a legitimate end.”

The appeals court concluded that Proposition 8, a 2008 ballot initiative that amended the state constitution to reverse a California Supreme Court decision allowing gay couples to marry, failed even this highly deferential test because it did not accomplish anything that was plausibly related to its ostensible goals.

Under California’s “domestic partnership” law, gay couples retain the same rights as straight couples, except for the right to call their relationship a marriage. Since Proposition 8’s sole effect was to remove that label, the court reasoned, its only justification was to mark gay marriages as morally inferior – an illegitimate end under the Equal Protection Clause.

This analysis is unlikely to apply elsewhere because California’s combination of a strong domestic partnership law with a constitutional amendment rescinding gay marriage rights is unusual, if not unique. But many other states’ gay marriage bans could be vulnerable under the heightened scrutiny that Obama applied to DOMA.

Obama may wish to avoid the implications of his constitutional logic until after the presidential election. But if the Supreme Court agrees to hear the California case this fall and asks the solicitor general to weigh in, that may not be possible.

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