With the potential extinction of threatened species, communities and species pools could become functionally and phylogenetically impoverished, especially if threatened species had distinct traits and evolutionary histories compared to least concern species. Alternatively, threatened species would have similar traits and evolutionary histories, and their extinction could imply the loss of functionally and phylogenetically 'redundant' species. We tested whether threatened plant species are functionally and phylogenetically rarer than least concern species. We considered two scales of plant assemblage (plots and species pools) from an intensively sampled temperate region (Czech Republic), using a sample of 23,072 vegetation plots classified into eight habitat groups. We analysed the traits and phylogeny of 1,730 species of angiosperms recorded in these plots. We found that the potential loss of threatened species could have minor functional and phylogenetic consequences for the communities in any habitat and at each assemblage scale. However, detailed analysis of individual traits revealed that some threatened species tend to have some unique trait value, such as being small and having lighter seeds. Phylogenetically unique species tended to be the most functionally rare, although this pattern was only weakly significant. This generally suggests similar conservation strategies for functionally rare and evolutionarily unique species. Policy implications. We show how novel tools related to functional rarity and phylogenetic uniqueness could be used to understand the role of threatened species in communities and different habitat types. This allows to understand which species and habitats could provide great functional and phylogenetic contributions to biodiversity to better guide management and conservation programmes. To fully achieve this potential, greater efforts in collecting functional trait information for threatened species remain urgent as well as considering both individual and combined trait information when estimating the functional originality of species.