The bronze statue that has stood at the museum's Central Park West entrance since 1940 depicts Roosevelt on horseback with a Native American man and an African man standing next to the horse.
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The statue has drawn protests over the years for depicting Black and Indigenous people as racially inferior.
Calls for the statue to be taken down have increased in the wake of George Floyd's death as protests and marches have broken out across the country, including in New York City.
"We have watched as the attention of the world and the country has increasingly turned to statues as powerful and hurtful symbols of systemic racism," museum president Ellen Futter told the New York Times.
Mayor Bill de Blasio said that the museum asked to remove the statue and he agrees it is the right decision:
"The American Museum of Natural History has asked to remove the Theodore Roosevelt statue because it explicitly depicts Black and Indigenous people as subjugated and racially inferior. The City supports the Museum's request. It is the right decision and the right time to remove this problematic statue."
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President Trump disagreed with the decision, tweeting "Ridiculous, don't do it!"
Officials said it hasn't been determined when the Roosevelt statue will be removed and where it will go.
Futter said the museum objects to the statue but not to Roosevelt, a pioneering conservationist whose father was a founding member of the institution and who served as New York's governor before becoming the 26th president. She said the museum is naming its Hall of Biodiversity for Roosevelt "in recognition of his conservation legacy."
In 2017, protesters splashed red liquid on the statue's base to represent blood and published a statement calling for its removal as an emblem of "patriarchy, white supremacy and settler-colonialism."
The Associated Press contributed to this report.