We assessed the effectiveness of a protected area (PA) network in representing tree taxonomic and phylogenetic uniqueness in subtropical Atlantic Forests (Rain, Mixed and Seasonal Forests). Using a network of plots distributed over ∼95,000 km2 in southern Brazil, we first map the distribution of species richness (SR), beta diversity (BD) and phylogenetic diversity (PD) across the extent of remaining forest in the region. We then tested whether areas of taxonomic and phylogenetic uniqueness are either over- or under-protected based on the existing PA network (3% coverage) and at least 10% coverage, and assessed whether protection is distributed equally for each uniqueness area type. Here, areas of taxonomic uniqueness were defined as those with higher contribution than the mean to the total BD, and areas of phylogenetic uniqueness as those with higher or lower PD than expected by chance given their SR, and sites exhibiting spatial congruence or mismatch between PD and SR. We found a high percentage of representation of both areas of uniqueness across the extent of remaining forest. However, our analyses showed that these areas are poorly and unequally captured by the PA network; they are on average less protected than expected based on at least 10% coverage and have high inequality of protection. Our results suggest that both beta diversity and evolutionary history of angiosperm trees are not adequately protected, and indicate relevant areas to extend the current PA network. We also emphasize the need to consider a multifaceted approach to maximize protection of the Atlantic Forest biodiversity.