Patch size, isolation, and vegetation structure are expected to strongly affect species persistence in fragmented landscapes, particularly for those with \30% of native habitat remaining. Those influences should be modulated by species characteristics, resulting in complex relationships. In order to investigate how species, habitat structure and landscape factors are related and how they affected species persistence, we studied bird communities in a fragmented Atlantic Forest region. Patch size strongly affected species richness and population abundances. However, some functional groups were more affected than others, particularly endemic and understory insectivores, species that are near the limits of their geographical distribution, those using few forest types, and those with their center of abundance in high altitude tropical forests. The effect of vegetation structure was mainly at the species level, reflecting specific responses to habitat quality. The importance of landscape variables varies according to the species group. For the most affected ones, which usually have low dispersal capacity, patch size and quality were the most relevant factors, whereas patch isolation was associated with the richness of groups with more generalist species. This pattern is due to the limited structural connectivity in the study region, composed of low matrix permeability (e.g. pastures and sugar cane), which isolate the most affected species, making them more dependent on local factors. In such a fragmented landscape, the largest patches should be prioritized for conservation purposes, as they aggregate the most vulnerable species and present the highest alpha diversity. Landscape management, as such, should also reconnect large fragments through corridors Electronic supplementary material The online version of this article (or matrix improvements, promoting better conditions for long-term persistence of the most affected species.