Samper, 46, a internationally-known conservation biologist, will become president and CEO of the Wildlife Conservation Society, which is headquartered at the Bronx Zoo in New York City.
In a statement to the Smithsonian Board of Regents, which is meeting Monday, Samper said he had always planned to stay about a decade.
“We have recruited the next generation of research curators, established an endowed fellowship program, and invested more than $100 million in our collections and the expansion of the Museum Support Center,” said Samper.
Samper was also acting Secretary of the Smithsonian from March 2007 until July 2008, following the controversial resignation of Lawrence Small.
The Natural History Museum is the largest natural history collection in the world, with 126 million objects from fossils to dinosaur bones to mummies to birds collected by John Audubon to the Hope Diamond.
Its building on the National Mall attracts about 7 million visitors each year.
During his tenure Samper oversaw the renovation of more than half of the exhibtions, including the Mammal Hall and the Human Origins hall, as well as the innovations of the Ocean Hall and the Butterfly Pavilion. In the fund-raising arena, Samper and the staff raised more than $180 million and tripled the museum’s endownment.
He is co-founder of the Encyclopedia of Life, a global effort to provide online knowledge about all life on Earth.
A native of Colombia, Samper also served as deputy director and staff scientist at the Smithsonian Tropical Research Institute in Panama.
Wildlife Conservation, a 117-year-old organization, has 4,000 employees and more than 500 research projects in 60 countries. Its budget is $200 million. Besides the Bronx Zoo, the group runs the Central Park Zoo, the Prospect Park Zoo, the Queens Zoo and the New York Aquarium.