Human activity is accelerating rates of extinction around the world, and there is therefore an urgent need to understand the potential consequences of species loss on functional diversity and ecosystem functioning. It is frequently assumed that the extinction of threatened species, which are usually rare species, may have limited effects on ecosystem functioning, especially within highly diverse regions, given the low abundance of individuals of each species and the potentially high functional redundancy among them. However, these rare species may contribute unique and irreplaceable functional roles, and therefore their extinction could have disproportionate impacts on ecosystems. We assess the functional importance of highly threatened anurans (frogs and toads) and then explore how the loss of these threatened species would impact spatial patterns of β-diversity in Ecuador, a hotspot of anuran biodiversity and endemism. We found that highly threatened species are, on average, more functionally distinct at an assemblage level than are less threatened anurans. We then show that the potential extinction of these highly endangered species would drive the taxonomic, phylogenetic, and, especially, functional homogenization of anuran assemblages across the Ecuadorian Andes. We suggest this could lead to profound alterations in the stability of local ecosystem functioning. Finally, we highlight the limited scope of the existing network of protected areas in Ecuador to effectively cover anuran assemblages predicted to become increasingly functionally homogenous. Our study underscores the potential losses of functional diversity that accompany species extinctions and the importance of considering the many facets of biodiversity in conservation decision-making.