Indonesia, located in Southeast Asia, is the world’s largest tropical island country. It is globally recognized as a unique center of biodiversity in the Asian–Australian transitional zone. To date, however, no national plant checklist of Indonesia has been published. Here, we collected botanical information on the flora of Indonesia and presented for the first time a checklist of known native species of vascular plants in the country. Our checklist included 30,466 species belonging to 2968 genera and 317 families, representing 8.7% of the 351,180 vascular plant species worldwide. Among the seven regions, Sumatra had the highest number of species at 10,902, followed by Indonesian New Guinea (9935), Java (9289), Kalimantan (9191), Sulawesi (7048), Maluku (5294), and Lesser Sunda Islands (4514). In contrast, Indonesian New Guinea had a much higher proportion of locally endemic species than other regions (59%). The seven regions were divided into three phytogeographical areas: the Sunda Shelf, the Sahul Shelf, and the Wallacea, based on similarities in floristic composition. Our checklist for Indonesia provides basic information for biodiversity conservation and associated research.