Acer rubrum L. and Liriodendron tulipifera L. are prolific throughout their ranges in the Southeastern U.S. and also have increasingly important roles in forestry and wood products in this region. The relatively low density and intermediate strength of the wood makes them versatile for use in many different wood products. Exploring the genetic structure of these species could provide a foundation for further genetic and breeding exploration with these economically important trees. This study utilizes amplified fragment length polymorphism to determine the level of genetic diversity of these species in contrasting physiographic provinces. AFLP was performed using five primer combinations on samples collected from six unmanaged populations of each species in the Mountains and Coastal Plain of the Southeastern U.S. Wood density was determined using an X-ray densitometer. A. rubrum lacked strong genetic structure while L. tulipifera showed differentiation between physiographic provinces. Genetic diversity of A. rubrum was lower within the Mountain populations (He: 0.327) than the Coastal Plain populations (He: 0.365). The average wood density for A. rubrum is lower in the Mountains (539.00 kg/m^3) than in the Coastal Plain (575.43 kg/m^3). Genetic diversity of L. tulipifera was higher overall (He: 0.289) than within the Mountain populations (He: 0.281) or the Coastal Plain populations (He: 0.271). The average wood density for L. tulipifera is greater in the Mountains (445.45 kg/m^3) than in the Coastal Plain (441.67 kg/m^3).