The interactive effects of forest disturbance and fragmentation on tropical tree assemblages remain poorly understood. We examined the effects of forest patch and landscape metrics, and levels of forest disturbance on the patterns of floristic composition and abundance of tree functional groups within 21 forest fragments and two continuous forest sites in southern Brazilian Amazonia. Trees were sampled within 60 (10 × 250 m) plots placed in the core areas of the fragments. Tree assemblage composition and abundance were summarized using nonmetric multidimensional scaling (NMDS). Forest patch size explained 36.2 percent and 30 percent of the variance in the proportion of small‐seeded softwood and hardwood stems in the 21 forest patches, respectively. Large fragments retained a higher abundance of hardwood tree species whereas small‐seeded softwood trees appear to proliferate rapidly in small disturbed fragments. Generalized linear mixed models showed that time since fragmentation had both positive and negative effects on the density of different functional groups of trees and on the ordination axes describing tree abundance. The composition and abundance of different tree genera were also related to time since fragmentation, distance to the nearest edge, and fire severity, despite the recent post‐isolation history of the forest patches surveyed. Both the proliferation of fast‐growing pioneer trees and the decline of hardwood trees found in our forest plots have profound consequences on the floristic composition, forest dynamics, carbon storage, and nutrient cycling in Amazonian forest fragments.