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This checklist includes, as rigorously as possible, all the known terrestrial and freshwater, i.e. insular, fungi, plants and animals of the Madeira and Selvagens archipelagos with the indication of their known presence on the islands of Madeira, Porto Santo, Desertas and Selvagens. It results from the collaborative work of many taxonomists from different Portuguese and foreign institutions (about 90 taxonomists), under the editorial coordination of the Azorean Biodiversity Group (http://www.gba.uac.pt). The total estimated number of terrestrial species and subspecies in the Madeira and Selvagens archipelagos was about 7,571 (7,452 species and 421 subspecies). Fungi and plants represent about 42% of the terrestrial diversity. However, animals dominate, arthropods being the majority (51%) of all recorded taxa. The total number of endemic species and subspecies from the Madeira and Selvagens archipelagos is about 1,419 (1,286 species and 182 subspecies), which represents 19% of the overall species diversity. The animal Phyla are the most diverse in endemic taxa, namely Mollusca (210) and Arthropoda (979), comprising about 84% of the Madeiran endemics. The percentage of endemism within Mollusca is particularly remarkable, reaching 71%. Within vascular plants there are 154 endemic species and subspecies (13% of the overall plant species diversity) while the remaining higher taxonomic groups are less diverse in terms of endemic forms: Fungi – 36 (5%); Lichens – 12 (2%); Bryophytes – 11 (2%); vertebrates 15 (24%).