The total number of hitherto ascertained species of vascular plants for the territory of National Park Mavrovo is encircled to 1,435 species, 404 of which are included in the category of medical plants.

From biogeofraphical point of view, the territory of the National Park Mavrovo, within the frames of the Republic of Macedonia, represents a core area for development of numerous arcto-mountain and boreal plant species.

Besides the high level of species diversity, another striking feature of the flora in the National Park is its high degree of endemism, represented by 13 endemic species, as well as the presence of rare plant species, 29 of which on national level, only on the territory of the National Park Mavrovo have been recorded.

The most striking feature of Biodiversity in the National Park Mavrovo is its high degree of species diversity. Floral and faunal elements with Ponto-Mediterranean (Eastern-Mediterranean) biogeographic origin are dominant, followed by the Complex of species with Boreal (Siberian) and Oreo-Tundral (Arctic-Mountain) origin, of which the Palaeo-Mountain (relict-mountain) sub-complex is more frequent and abundant in comparison with species of the sub-complex with of Arctic (tundral) origin. The Complex of species with Eremial (steppes, semi deserts/deserts) origin is less represented.

The assessment and evaluation of Biodiversity are made on the basis of numerous representative taxonomic groups of flora and fauna that include in total 3,757 taxa (species and subspecies) represented by: 78 algae, 661 fungi, 151 lichens, 1,473 vascular plants, 1,172 invertebrates, 8 fishes, 11 amphibians, 24 reptiles, 129 birds and 50 mammal species.

Habitats Directive (Directive 92/43/EEC) provides Legal Protection under Annex II for 20 species (eight species of invertebrates, two species of amphibians, three species of reptiles and seven species of mammals), which means that the species are of community interest whose conservation requires designation of special areas of conservation.

Habitats Directive (Directive 92/43/EEC) also provides Strict Legal Protection under Annex IV for additional 45 species (one vascular plant, seven invertebrates, six amphibians, 18 reptiles, and 13 species of mammals).

The Wild Birds Directive-WBD (Directive 2009/147/EC) of the European Parliament and the Council of the European Union provides Legal Protection for 19 species of birds (listed in Annex I), through the establishment of a coherent network of Special Protection Areas (SPAs) comprising all the most suitable territories for these species. Seven species listed in Annex I and one species listed in Annex II of the WBD are included in Category VU (Vulnerable) concerning the European Threat Status of birds (ETS). Two species of birds are included in the Category SPEC1 and seven species in the Category SPEC2 in accordance with the European Conservation Status of Birds (SPECs).

The IUCN Red List of Globally Threatened Species (2011) includes five threatened species, all in the Category VU (Vulnerable), of which three species of invertebrates: Astacus astacus, Austropotamobius torrentium and Parnassius apollo; one species of reptiles: Vipera ursinii; and one species of mammals: Dinaromys bogdanovi.

The IUCN European Red List of Butterflies (2010) includes two threatened species, of which the species Phengaris arion is included in the Category EN (Endangered), while the species Euphydryas maturna in the Category VU (Vulnerable).

The IUCN European Red List of Reptiles (2009) includes one threatened species: Vipera ursinii in the Category VU (Vulnerable).

Within the boundaries of the Park, presence of 115 endemic taxa (species and subspecies) has been ascertained, of which: 13 vascular plants, 86 invertebrates, three fishes, three amphibians, five reptiles and 5 mammals. Of the total number of 115 endemic taxa, 58 taxa are local/national endemics, while the remainder 57 taxa are Balkan endemics

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