Auffenberg received his M.Sc. from the University of Florida in 1953 with his thesis A Study of Geographic Morphological Variation in the Blacksnake. He held a temporary position as Curator of Vertebrate Paleontology at The Charleston Museum in 1954 and a Special Student in Paleontology at Harvard University in 1955–56; obtaining his doctoral degree at the University of Florida in 1956.[2] He wrote his dissertation on the fossil snakes of Florida.[3]