The administration said the ban in California's Proposition 8 violates the U.S. Constitution's guarantee of equal protection.
The government's brief said private individuals, "committed gay and lesbian couples, seek the full benefits, obligations, and social recognition conferred by the institution of marriage. California law provides to same-sex couples registered as domestic partners all the legal incidents of marriage, but it nonetheless denies them the designation of marriage allowed to their opposite-sex counterparts.
"Particularly in those circumstances, the exclusion of gay and lesbian couples from marriage does not substantially further any important governmental interest," the brief said. "Proposition 8 thus violates equal protection."
In a statement, U.S. Attorney General Eric Holder said: "In our filing today in Hollingsworth vs. Perry, the government seeks to vindicate the defining constitutional ideal of equal treatment under the law. Throughout history, we have seen the unjust consequences of decisions and policies rooted in discrimination. The issues before the Supreme Court in this case and the [separate] Defense of Marriage Act case are not just important to the tens of thousands Americans who are being denied equal benefits and rights under our laws, but to our Nation as a whole."
California voters approved Proposition 8, the California Marriage Protection Act, in 2008 with slightly more than 52 percent for, nearly 48 percent against. Prop 8 says in part, "Only marriage between a man and a woman is valid or recognized in California."
A federal judge declared Prop 8 unconstitutional and a three-judge appeals court panel in San Francisco agreed 2-1.
Argument in the U.S. Supreme Court in Hollingsworth vs. Perry is scheduled for March 26. The DOMA challenge is scheduled to be heard the next day.
California Gov. Jerry Brown, when he was state attorney general, refused to defend Prop 8. ProtectMarriage -- its sponsor is a state non-profit, California Renewal -- is the official proponent of the proposition and has been allowed to defend it in the Supreme Court.
Earlier this week, the California state attorney general's office filed a brief urging the high court to strike down the ban.
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