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• The IUCN Red List of Ecosystems criteria were applied at the national scale. • 157 types of natural and semi-natural habitats of the Czech Republic were assessed. • Two habitats were Collapsed, 14 Critically Endangered, 33 Endangered, 33 Vulnerable. • Natural succession after abandonment, eutrophication and drought are major threats. • IUCN Red List of Ecosystems criteria are applicable in small countries or regions. The Red List of Habitats of the Czech Republic assesses the risk of collapse for 157 types of natural and semi-natural habitats defined in the second edition of the Habitat Catalogue of the Czech Republic. The assessment followed the guidelines for the IUCN Red List of Ecosystems as used in the European Red List of Habitats project, using the criteria of habitat reduction in quantity, restricted geographic distribution, and reduction in abiotic and biotic quality. Quantitative data for the assessment were partly taken from a detailed field habitat mapping at the national scale, and where no quantitative information was available, the values were estimated by summarizing independent judgements of 17 experts. In addition to the criteria involved in the Red List assessment, the experts also assessed various types of threatening factors and their importance for each habitat. Of 157 assessed habitats, 2 were Collapsed (CO), 14 Critically Endangered (CR), 32 Endangered (EN), 33 Vulnerable (VU), 30 Near Threatened (NT) and 46 Least Concern (LC). The largest proportion of CR + EN habitats was in the habitat group of springs and mires and in the group of wetlands. The threatening factors evaluated as the most important were successional changes after cessation of traditional management, eutrophication due to atmospheric nutrient deposition and pollution from agriculture, and increased drought in water-dependent habitats due to climate change or changes in local hydrological regime. The study shows that the IUCN criteria for Red List assessment of habitats, although developed for the global scale, are also applicable within small countries or regions. [ABSTRACT FROM AUTHOR]