One of the first and most essential steps in the identification process of the Natura 2000 network is the establishment of the habitats and species reference lists in the country. Annex I of Birds Directive and Annexes I, II and IV of Habitats Directive (for some species as plant species and fish species, also consider Annex V) list the species that are the reference for the designation of SPAs and pSCI. Not all species listed in these Annexes occur in Serbia, so specific reference lists for each species and habitat have been established.

The reference list of plant species in Serbia counts 33 species from Annex II and Annex IV and 34 species from Annex V of the Habitats Directive. For this list of species, five of them: Campanula secundiflora, Cephalaria pastricensis, Daphne malyana, Nepeta rtanjensis and Picea omorika are given as a proposal for amendments to the Annexes of Habitats Directive.

Animal species – Vertebrates

The reference list of birds contains the species from Annex I of Birds Directive and migratory species. It has been prepared in a consensus with Serbian experts, although not current and detailed information is available for all the species. From 197 species and sub-species of birds listed in Annex I, 141 species are included in the Serbian Reference List.

For these species Member States must conserve their most suitable territories in number and size as Special Protection Areas.

Of the 141 species of mammals protected in Europe through Annexes II and IV of Habitats Directive, 46 are present in Serbia. Of these species, 31 are species of bats and 15 other mammals. However, only 2 species have an unclear status, and more research to confirm their presence in Serbia is needed. For these 46 species there are 3 of them that are not yet included in the Annexes of Habitats Directive, and they are part of the amendments to the Habitats Directive that Serbia has submitted, specifically, the species: Canis lupus, Felis sylvestris and Rupicapra rupicapra balcanica.

The Habitats Directive lists 71 amphibian species under protection; however, only 14 species occur in Serbia. Most of them are distributed in the two biogeographical regions, Pannonian and Continental ones, except a couple of newts species that are not present in the Pannonian region. Serbia has amended the Habitats Directive to include the species Triturus dobrogicus as part of the Annex IV.

The reference list includes 21 species, although 106 are included in the Annexes of Habitats Directive. Serbia has amended the Habitats Directive to include the species Vipera berus bosniensis as part of the Annex IV.

There are 203 fish species under protection in Europe. From this list of species, 34 are included in the reference list of fish species, although one of them is considered extinct in the Danube river, hence in Serbia.

Animal species – Invertebrates

The group of species include in the Annexes of Habitats Directive and those present in Serbia are the following ones:

The European Directive is protecting 134 species of invertebrate species, although only half of them (67) occur in Serbia, and some of them are still in an unclear confirmation of their presence in the country. The Republic of Serbia has amended the Habitats Directive to include the species Palingenia longicauda, an aquatic insect from order Ephemeroptera which is also known as the Tisza mayfly. This species is distributed in Tisza River (in Slovakia, Serbia and Hungary, although the presence in Slovakia is not confirmed). Also, Serbia has amended the Habitats Directive for the inclusion of three more species of invertebrates: two grasshoppers; Pyrgomorphula serbica and Zeuneriana amplipennis and one beetle species; Tentyria frivaldszkii.