With decreasing population sizes and fragmentation of the original habitats of pteridophytes in Hainan Island, the abundance of most pteridophytes has been dramatically reduced, and some species may be at the brink of extinction. To assess the natural distribution of pteridophytes on Hainan Island, we conducted three analyses: flora, niche, and habitat. Thirty-two species of endangered pteridophytes in 21 families were found in Hainan Island, accounting for 8% of the 400 pteridophytes species there. Floristic studies showed that 9% of these 32 species are tropical, 50% are tropical Asian, 20% are pan-tropical, 3% are from East Asia, 3% from the Southern Hemisphere, and 15% are endemic to Hainan Island. Niche analysis showed that 21 of the 32 species (66%) are epiphytic or semi-epiphytic, while 11 (34%) are terrestrial. About 24 species of endangered pteridophytes are distributed in protected, conservation regions and the others are distributed partly in the conservation and non-conservation regions. In species-poor families (< 6 species), most of the species are endangered.