Commissioned by the Ministry of the Environment of the Czech Republic, the Agency for Nature Conservation and Landscape Protection of the Czech Republic has proposed a new Specially Protected Species list. The original list had been developed in 1992 and consequently it was amended only once, namely because of the transposition of the species listed in Annex IV to Directive No. 92/43/EEC on the conservation of natural habitats and of wild fauna and flora, commonly known as the Habitats Directive, to the national legislation. When developing the new list, it was necessary to take into account risk of extinction and rarity of the individual species and habitats to which they are related, direct threats possessed by human activities as well as the need for special conservation management. Including into the Czech Republics Red Lists of threatened species was a basic criterion. At the same time, umbrella species (species with large area requirements for which protection of the species offers protection to other species including less known and less conspicuous that share the same habitat) were also preferred. When drafting a list of specially protected invertebrates, due to high species richness within the group, other criterion was their determinability. Among fungi, only macromycetes (larger fungi, macrofungi) were included into the proposed Specially Protected Species list as well as macrolichens. The current decree includes 849 taxa, while the proposed one nearly 1,400 items. A rapid increase in the listed species occurred in all the groups except vertebrates, while lichens and mosses are newly listed there.