Stebbins started graduate studies at Harvard in 1928, initially working on flowering plant taxonomy and biogeography—particularly that of the flora of New England—with Merritt Lyndon Fernald. He completed his MA in 1929 and continued to work toward his Ph.D. He became interested in using chromosomes for taxonomic studies, a method that Fernald did not support. Stebbins chose to concentrate his doctoral work on the cytology of plant reproductive processes in the genus "Antennaria", with cytologist E. C. Jeffrey as his supervisor and Fernald on his supervisory panel. During his Ph.D. candidature, Stebbins sought advice and supervision from geneticist Karl Sax. Sax identified several errors in Stebbins's work and disapproved of his interpretation of results that, while in accordance with Jeffrey's views, were inconsistent with the work of contemporary geneticists. Jeffrey and Sax argued over Stebbins's dissertation, and the thesis was revised numerous times to accommodate their differing views.