The location of the nutrient-rich organic refuse produced by a leaf-cutting ant colony varies among ant species. Atta cephalotes locate their organic refuse in subterranean chambers, whereas A. colombica place their organic refuse on the soil surface near the nest. We studied the effect of the absence or presence of external organic refuse on the abundance of fine roots and seed bank composition in the superficial horizons of ant nests. We sampled soils from ant nests or dumps and adjacent areas of 15 adult nests of A. cephalotes at La Selva (LS), Costa Rica, and of 15 of A. colombica nests on Barro Colorado Island (BCI), Panama. Soils from A. cephalotes nests did not differ from adjacent soils in abundance of fine-root and seed diversity. In contrast, organic refuse from A. colombica nests was less diverse in seed composition (due to the great abundance of Miconia argentea) and had a greater abundance of fine roots than adjacent areas. Thus the external location of the ant-nest organic refuse is potentially important in determining the different types of plant recolonization in abandoned or dead ant nests. The relative abundance of these Atta species may influence the structure and/or composition of tropical forests.