Quercus ellipsoidalis (Hill's oak), an endemic of east-central North America, is morphologically similar to Q. coccinea (scarlet oak) and is subsumed into that species in several floristic treatments. This study uses data from more than 250 amplified fragment length polymorphism (AFLP) markers to investigate whether Q. coccinea and Q. ellipsoidalis are genetically distinct from one another. Whereas Q. coccinea and Q. ellipsoidalis separate from one another in all analyses, Q. velutina (black oak) populations collected from the geographic range of both Q. coccinea and Q. ellipsoidalis do not separate out by geographic region. This, combined with the strong differentiation between Q. coccinea and Q. velutina but weak differentiation between Q. ellipsoidalis and Q. velutina, supports the view that Q. coccinea and Q. ellipsoidalis are not simply regional variants of a single taxon. Moreover, while there is no evidence from the molecular data we collected of hybridization between Q. coccinea and Q. ellipsoidalis, the data suggest that there may be gene flow between Q. ellipsoidalis and Q. velutina. A clearer understanding of the relationships among these taxa is essential to understanding the taxonomy of Quercus section Lobate in eastern North America.