Witkin was elected as a member of the National Academy of Sciences in 1977, at the time she was one of the few women elected to the Academy; a Fellow of the American Academy of Arts and Sciences (1978), a Fellow of the American Association for the Advancement of Science (1980); and a Fellow of the American Academy of Microbiology. She was awarded the 2000 Thomas Hunt Morgan Medal and her contributions to science have been recognized by the United States government as she was awarded the National Medal of Science in 2002;