Thanks to its geographic location, variety of natural conditions and the cultural-historical development of its constituent parts, the Czech Republic is characterised by a great richness of plant (including fungal, moss and lichen) and animal species and their communities. Overall, more than 2,700 species of vascular plants, 2,400 species of non-vascular plants, 50,000 species of invertebrates, and some 380 species of vertebrates have been identified in the country. According to the current national Red Lists, expressing the degree of endangerment of species, around 34% of mammals , 52% of nesting birds , 50% of reptiles , 43% of amphibians , 43% of fish , 60% of vascular plants and 43% of non-vascular plants are threatened in the Czech Republic. Effective plant and animal protection, including protection of habitats, is the prerequisite for assuring biodiversity protection at the species level. In the Czech Republic, this protection is anchored in legislation primarily by Act no. 114/1992 Coll., on nature and landscape protection, as amended. This Act defines a number of instruments that aid in the protection of plant and animal species. It defines general protection of all plant and animal species, and separately protection of wild birds and special protection of selected, rare, or scientifically and culturally significant plant and animal species. The protection of trees and memorial trees can also be considered a type of protection of a selected category of plants. Action Plans are implemented for species threatened by extinction in the form of comprehensive packages of measures that eliminate or reduce known threatening factors and improve the conditions for life of such species. Management Plans are similar strategic documents, prepared for less severely endangered species for which there is a risk of change in their conservation status, or for species requiring a comprehensive co-ordinated approach due to their socio-economic importance or impacts.
The instruments in so-called territorial protection also contribute to the protection of species and, most importantly, their habitats at both the general (territorial system of ecological stability, important landscape elements) and specific levels (specially protected areas: national parks, protected landscape areas, nature reserves and nature monuments). Protection of plants, animals, and their habitats is also largely the purpose of the relevant EU Directives (Council Directive 79/409/EEC on the conservation of wild birds, and Council Directive 92/43/EEC on the conservation of natural habitats and of wild fauna and flora) and the Natura 2000 system established under them (comprising so-called Specially Protected Areas and Special Areas of Conservation).
The proliferation of non-native, invasive plant and animal species is a specific area closely related to both biodiversity protection and species and habitat protection. Globally, biological invasions are considered as one of the most important factor (after direct habitat destruction and fragmentation) leading to loss of biodiversity and species extinction. At the same time, proliferation of invasive species has numerous economic and social impacts. The situation in the Czech Republic, and broadly in Central Europe, is not as critical as elsewhere (such as New Zealand and Australia); still there are numerous cases of biological invasions with significant impacts. The best-known invasive species include the giant hogweed, knotweeds, non-native crayfish species, and the American mink.