Tropical forests are being cleared at an accelerating rate, despite being one of the most important habitats for global biodiversity. Many remaining tropical forest tracts are now highly degraded and fragmented, which presents a major problem for sensitive and threatened forest-dwelling species that depend on this habitat for survival. In this study, we assessed the impacts of forest fragmentation, and its associated edge-effects, on tree species diversity, tree size, and structural diversity within the transitional forests of north west Madagascar. Using data collected from 9,619 trees within 200 vegetation plots, we calculated species diversity indices, a range of dendrometry measurements, and Shannon-Weaver diversity indices of structure, which we compared among core and edge areas of a continuous forest and a fragmented forest. We found that species diversity, tree size, and structural diversity was significantly reduced in fragmented forest, and within forest edge areas in comparison to core, continuous forest. We also observed species diversity and structural diversity to be strongly influenced by the total size, core area size, and shape of forest fragments. Whilst we found fragmentation and edge-effects to individually impact tree species diversity, size and structural diversity, fragmentation and edge-effects are strongly correlated and affect natural forest synergistically. Our results provide evidence that forest fragmentation seriously degrades habitat quality and integrity of transitional forests, which is of great concern for the threatened species that inhabit them. Urgent conservation efforts are needed to halt ongoing forest fragmentation throughout the tropics, and reforestation and restoration efforts are required to reconnect isolated forest patches and to reduce forest edge area.