The Stonewall National Monument will be anchored by Christopher Park, a small park just across from the iconic Stonewall Inn tavern, and covers a 7.7 acre swath of Greenwhich Village where the uprising took place after police raided the gay bar in 1969.
Obama said the monument would "tell the story of our struggle for LGBT rights" and of a civil rights movement that became a part of America.
To herald the new monument, the video of Obama along with footage from the uprising was to be played at noon tomorrow on the billboards in Times Square just as New York's annual pride celebration is getting under way, the White House said.
The declaration also comes as advocates celebrate the one-year anniversary on Sunday of the Supreme Court decision legalizing gay marriage nationwide.
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In addition to the Supreme Court decision, since the 1969 uprising the US has enacted anti-discrimination protections, allowed gays and lesbians to serve openly in the US military and seen prominent athletes and entertainers come out of the closet.
It also comes as the gay community comes to grips with a fresh and agonizing reminder of ongoing threats to their safety. In announcing the monument, the White House said the mass shooting at a gay bar in Orlando, Florida, illustrated that LGBT people still 'face acts of violence, discrimination and hate."
"Stonewall is finally taking its rightful place in American history," said Rep. Jerrold Nadler, D-N.Y., who had advocated for federal recognition for the site.