Large tree species have a disproportional influence on the structure and functioning of tropical forests, but the forces affecting their long-term persistence in human-dominated landscapes remain poorly understood. Here we test the hypothesis that aging forest edges and small fragments (3.4–295.7 ha) are greatly impoverished in terms of species richness and abundance of large trees in comparison to core areas of forest interior. The study was conducted in a hyper-fragmented landscape of the Atlantic forest, northeast Brazil. Large tree species were quantified by recording all trees (DBH ≥ 10 cm) within fifty-eight 0.1-ha plots distributed in three forest habitats: small forest fragments (n = 28), forest edges (n = 10), and primary forest interior areas within an exceptional large forest remnant (n = 20). Large tree species and their stems ≥10 cm DBH were reduced by half in forest edges and fragments. Moreover, these edge-affected habitats almost lacked large-stemmed trees altogether (0.24 ± 0.27% of all stems sampled), and very tall trees were completely absent from forest edges. In contrast, large trees contributed to over 1.5% of the whole stand in forest interior plots (2.9 ± 2.8%). Habitats also differed in terms of tree architecture: relative to their DBH trees were on average 30% shorter in small fragments and forest edges. Finally, an indicator species analysis yielded an ecological group of 12 large tree species that were significantly associated with forest interior plots, but were completely missing from edge-affected habitats. Our results suggest a persistent and substantial impoverishment of the large-tree stand, including the structural collapse of forest emergent layer, in aging, hyper-fragmented landscapes.