"Closer now to 80 than 79, the passing on of my remaining vestiges of leadership is more than overdue," said Watson, who won a Nobel Prize in 1962 for discovering, along with Francis Crick, the double-helix structure of DNA.
"The circumstances in which this transfer is occurring, however, are not those which I could ever have anticipated or desired."
In London earlier this month to promote a new book, Watson was quoted in the Sunday Times Magazine of London as saying that he's "inherently gloomy about the prospect of Africa" because "all our social policies are based on the fact that their intelligence is the same as ours - whereas all the testing says not really."
Watson added that while he hopes everyone is equal, "people who have to deal with black employees find this is not true."
He also said people should not be discriminated against on the basis of color, because "there are many people of color who are very talented."
Watson stepped down from his post as chancellor of the Cold Spring Harbor Laboratory, which was founded on the north shore of Long Island in 1890 and has been home to seven Nobel Prize-winning scientists. Its board of directors suspended Watson after his remarks were made public last week.
On Thursday, chairman Eduardo Mestre said the board respected Watson's decision to retire.
"For over 40 years, Dr. Watson has made immeasurable contributions to the laboratory's research and educational programs," Mestre said. "His legacy as 1962 Nobel Prize laureate for describing the structure of DNA will continue to influence biomedical research for decades to come."
Watson apologized for his remarks in London before cancelling the remainder of the tour to promote his new book, "Avoid Boring People: Lessons From a Life in Science."
In a written statement to The Associated Press last week, Watson said he was "mortified by what had happened."
"To all those who have drawn the inference from my words that Africa, as a continent, is somehow genetically inferior, I can only apologize unreservedly," he said. "That is not what I meant. More importantly from my point of view, there is no scientific basis for such a belief."
Watson is no stranger to controversial scientific views. In 2000, in a speech at the University of California, Berkeley, he suggested that sex drive is related to skin color. "That's why you have Latin lovers," he said, according to people who attended. "You've never heard of an English lover. Only an English patient."
Some years earlier he was quoted in a newspaper as saying, "If you could find the gene which determines sexuality and a woman decides she doesn't want a homosexual child, well, let her."