Frank Ellis Boynton (July 10, 1859 – December 10, 1942) was a self-taught American botanist active in the Southeastern United States. He worked at Biltmore Estate with his brother, Charles Lawrence Boynton, and Chauncey Beadle. Boynton's dewberry, Rubus boyntonii was named in honor of Frank Ellis Boynton. The standard author abbreviation F.E.Boynton is used to indicate this person as the author when citing a botanical name.