Watson, one of the most influential scientists of the 20th century, had apologised after making similar comments to a British newspaper in 2007.
However, the laboratory's decision to revoke Watson's honours and titles is the result of American Masters: Decoding Watson, a PBS documentary that aired in the U.S. earlier this month. The laboratory revoked three honorary titles, including chancellor emeritus.
At the time, he was forced to retire from his job as chancellor at Cold Spring Harbor on Long Island, but he has retained his office there, as well as the titles of chancellor emeritus, Oliver R. Grace professor emeritus and honorary trustee.
In 2007, he said he was "inherently gloomy" about Africa's prospects because Western policies towards the continent assumed Africans were as intelligent as Europeans.
The remarks are the latest in a series of racist and homophobic statements that have tainted Watson's career.
In the film, Watson references a view that average IQ differences between blacks and whites reflect underlying genetic differences shaped by natural selection.
In the 2007 article Watson went on to avow that, while he wanted everyone to be equal in terms of intelligence, "people who have to deal with black employees find this is not true".
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The lab "unequivocally rejects the unsubstantiated and reckless personal opinions Dr James D Watson expressed on the subject of ethnicity and genetics", its president, Bruce Stillman, and chair of the board of trustees Marilyn Simons said in a statement.
In the PBS documentary, the host asked Watson if he had changed his views on race in the decade since his departure from the lab.
Speaking on a TV program which aired earlier this month, Watson reiterated his position that genes underlie racial differences on IQ tests.
In 1962, the team was awarded a Nobel Prize in Physiology "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material". "Nonetheless, the statements he made in the documentary are completely and utterly incompatible with our mission, values, and policies, and require the severing of any remaining vestiges of his involvement".
Dr Watson sold his gold medal in 2014, saying he had been ostracised by the scientific community after his remarks about race.
Watson and Crick's key evidence in their study, Photo 51, was produced by Franklin and her graduate assistant Ray Gosling at King's College London, and secured without Franklin's knowledge or authorisation via her supervisor, Maurice Wilkins.