In this study we surveyed all trees ≥10 cm diameter at breast height within 20 0.1 ha plots in a 3,500 ha forest fragment, surrounded by sugar cane fields, of the Brazilian Atlantic forest to compare tree species assemblages at the forest edge (0–100 m into forest) vs forest interior (>200 m). Plots were perpendicular to the margin. The mean number of tree species was significantly higher in the forest interior (35.4 ± SD 7.1 vs 18.4 ± SD 4.4). In addition, forest edge differed from interior in the proportion of shade-tolerant, emergent, large/very large-fruited species, and large-seeded tree species. Among the 134 tree species recorded, 24% were exclusive to the forest edge and 57% to the forest interior. Our results suggest that both the current system of protected areas and archipelagos of small fragments (1) tend to retain only a subset of the original flora, (2) will converge in terms of floristic and ecological composition (biotic simplification and homogenization), and (3) will lose rare and threatened tree species.