In 1959 he and his family moved to Boulder, Colorado to assist his former adviser, Arnold Grobman to start up the innovative and popular high school science program Biological Sciences Curriculum Study (BSCS). Missing time in the field, Auffenberg returned to Gainesville, Florida, the University of Florida in 1963 to assume the role of Chairman of the Natural Sciences Department and Curator of Herpetology at the Florida Museum of Natural History (then the Florida State Museum). He remained as chairman until 1971 when he stepped down to concentrate on research.