There are four known species of Isoetes (Family Isoetaceae) from China: I. hypsophila, I. sinensis and I. yunguiensis on the mainland, and I. taiwanensis on Taiwan. In a 4-year study we documented the distribution and habitat characteristics of all four species and evaluated their conservation status using IUCN criteria. All four species are facing a high risk of extinction and should be categorized as Critically Endangered on the IUCN Red List. Habitat degradation and loss, water pollution and eutrophication, competitive exclusion, and human disturbance are the main factors causing the decline and extirpation of Isoetes. Only I. taiwanensis is protected in situ in Yangmingshan National Park on Taiwan. None of the species or habitats of Isoetes on mainland China are presently protected, although all species have been designated by the government as State Key Protected Wild Plants. Our results suggest that conservation strategies should be implemented urgently, particularly on the mainland.