Species composition in three strata of 63 permanent plots across two physiographic divisions (Ozark Hills and Shawnee Hills) of the Shawnee National Forest (SNF) in southern Illinois was resampled 3–6 years after initial establishment with the objective to assess short-term changes in species composition. Environmental data collected at each plot included overhead canopy cover, elevation, solar radiation, slope, and a suite of nine soil properties. Basal area of the trees in the Ozark Hills Division did not change, but total basal area and basal area of Carya ovata, Fraxinus americana, Quercus rubra, and Ulmus alata increased in the Shawnee Hills Division. In the woody understory, there was an increase in the density of Acer saccharum, C. florida, F. americana, and U. alata in the Shawnee Hills Division, and a decrease in density of C. florida and Fagus grandifolia in the Ozark Hills Division. The decrease in C. florida in the Ozark Hills Division is likely due to an infestation of Discula destructive, a fungal pathogen. There was a significant change in the composition of the field layer from one sampling to the next including a change in the abundance of 16 species and an increase in total cover probably due to a lack of recent disturbance. The field layer had the largest number of environmental variables related to species composition (8 variables) when compared to the tree stratum (7) and the woody understory (5) with elevation being the single variable related to the composition of all strata. Overall, the changes reflect rapid and dynamic changes occurring in these forests that differ between the two physiographic divisions, especially in the woody understory and field strata.