Background We describe Rizoma, a new comprehensive online database on traditional uses of Chilean flora. The Rizoma database was built by reviewing multiple data sources on the uses of native plants and integrating phytogeographic and ecological aspects of plant species. This database attempts to safeguard traditional knowledge by making it available and visible to society, providing 1380 use records from 736 vascular plant species native to Chile. In addition, it contributes to a better understanding of the use patterns of Chilean native plants. New information The Rizoma database includes 1380 use records from 736 vascular plant species native to Chile, representing 399 genera and 128 families. Each species record provides information on geographic distribution, phytogeographic origin, life form, life span and use category. In addition, the online version includes information on the mode of use of each species, as well as common names and photographs. The database serves as a traditional knowledge repository that contributes to preserving local biological and cultural diversity for future generations.