The tree flora of southeastern Brazilian Atlantic forests was investigated according to two main aspects: (a) the variations in floristic composition of both rain and semi-deciduous forests were analyzed in terms of geographic and climatic variables by performing multivariate analyses on 125 existing floristic checklists; and (b) the links of both rain and semi-deciduous forests to Amazonian forests and Cerrados (woody savanna) were assessed. All analyses were performed at the species, genus, and family levels. The information obtained for the 125 forest areas was organized into an environmental database containing geographic and climatic records, and a floristic database containing binary presence records for 2532 species, 520 genera, and 106 families. Canonical correspondence analyses (CCA) were utilized to assess the relationship between geographic and climatic variables, and tree flora composition. Venn diagrams and cluster analyses were used to assess the floristic links to Amazonian forests and Cerrados. The following patterns were detected at all three taxonomic levels: (a) the differentiation between rain and semi-deciduous forests is floristically consistent and strongly correlated with rainfall regime, although transitions may be abrupt to gradual; (b) a north–south differentiation exists for both rain and semi-deciduous forests, probably caused by variations in both temperature and rainfall regime; (c) The flora of semi-deciduous forests also changes with increasing distance from the ocean and the associated increasing rainfall seasonality; and (d) elevation and associated temperatures are strongly correlated with the internal differentiation of both rain and semi-deciduous forests. To a considerable extent, the tree flora of semi-deciduous forests is a subset of the rain forest flora, probably extracting species that are able to cope with a longer dry season. There is greater floristic similarity at the species level between Atlantic rain and semi-deciduous forests than between any of these and either Amazonian rain forests or Cerrados. Nevertheless, semi-deciduous forests and Cerrados show stronger links, particularly at the generic and familial levels. Therefore, there is little floristic ground for viewing Atlantic rain forests as being closer to their Amazonian counterparts than to the adjacent semi-deciduous forests. The most appropriate view of rain and semi-deciduous forests in southeastern Brazil is that of a continuum in tree species distribution. We suggest that the definition of Atlantic forests should be as comprehensive as that of Amazonian forests.