The most striking features of the fauna in Pelister National Park are its diversity and heterogeneity, as well as the presence of many relict and endemic species. Endemic species are mainly registered in invertebrate groups of organisms.

Pelister’s Earth (Terrestrial) Invertebrate Fauna shows the presence of a total of 288 taxa, belonging to a total of 10 groups of invertebrates.

From invertebrates, a small glacial population of the Chirocephalus diaphanus carinatus, which represents the Balkan relict-endemic taxon, is found in the small glacial lake “Little Lake”.

The amphibian shrimp Niphragus pancici peristericus, a Pelister endemic, living only in this lake, lives exclusively in the large glacial lake “Big Lake”.

Only in the waters of these two glacial lakes is the harpacticoid shrimp Arcticocampus macedonicus, a Pelister endemic species.

In the natural waters of NP Pelister, at an altitude of between 1600 and 2200 m, live two Pelister relict-endemic species of Ostracodes: (Iliodromus peristericus and Eucypris diebeli).

Religious-endemic faunal elements are also present in the mountain streams and rivers of the National Park. The Macedonian endemic plexopathy (Nemoura peristeri) is described by the Magarevska River.

Several Pelister endemic species are present throughout the forest and high mountain belt, such as: the Pelister centipede (Brachydesmus peristerensis); Beetles: (Alpaeus macedonica, Cychrus attenuatus peristericus, Duvaliotes peristericus, Platyduvalius macedonicus, Trechus hajeki), Night butterfly (Hadena clara macedonica) and Small butterflies: (Scythris crypta and Scythris similis).

Among the vertebrates in Pelister, in addition exist 2 species of fish, are present  12 species of amphibians, 16 species of reptiles (or 50% or from the diversity of reptiles in RS Macedonia), 116 species of birds (5 of which are extinct) and 47 species of mammals.

There are two types of trout within the National Park. Only in the upper reaches of the rivers Sapundzica, Zlokukjanska and Rotinska rivers live the more accurate trout (Salmo pelagonicus), and in the Brajcinska River live the Pelister trout (Salmo peristericus) which are Pelister endemic species.

The high mountain belt of Pelister is inhabited by a specific fauna. which is a mosaic of relict Mediterranean high-mountain elements, then boreal, arcto-alpine and steppe faunal elements. The most striking species in this belt is the Balkan wild goat (Rupicapra rupicapra balcanica).

The Snowy meadow (Chionomys nivalis) lives on the rocky terrain. Through the wet meadows and pastures with lush vegetation you can see the Mountain lizard (Lacerta agilis), the Hinge (Vipera berus), the Coniferous meadow (Microtus subterraneus), the Eurasian pygmy shrew (Sorex minutus), the relict Mole (Talpa stankovici) and the Lesser mole-rat (Nannospalax leucodon).

Among the birds, the characteristic species for this belt are: the Red-headed gull (Pyrrhocorax pyrrhochorax), the Scapegoat (Monticola saxatilis), the White-tailed hedgehog (Turdus torquatus) and the Partridge (Alectoris graeca).

Four mammal taxa have been described for the first time by sites within the National Park: Balkan blind mole (Talpa caeca beaucournii), a typical inhabitant of moth forests. Balkan mole (Talpa stankovici), described on the basis of specimens collected from mountain meadows in the National Park. This species is registered as Macedonian – subendemite, because it is found in part in the border areas of Greece and Albania.
Macedonian leafy melon (Clethrionomys glareolus makedonicus), first recorded and described by the deciduous and mixed forests of Pelister, is also a Macedonian endemic. Macedonian meadow (Microtus felteni), described by the Pelister rainforests, is a Macedonian endemic because it has so far been registered only in the mountains of Western Macedonia.

Within the forest belt of the National Park, the following vertebrates are most often present:

 Fire Salamander (Saiamandra salamandra),
 Macedonian Crested Newt (Trituruis carnifex macedonicus),
 Agile Frog (Rana dalmatina),
 Stream Frog (Rana graeca),
 Tree Frog (Hyla аrharea),
 Common Hermann’s Tortoise (Testudo hermanni),
 Aesculapian Snake (Elaphe longissima),
 Smooth Snake (Coronella austriaca),
 Woodcock (Scolopax rusticola),
 Hazelhen (Bonasa bonasia),
 Eagle Owl (Bubo bubo),
 Tawny Owl (Strix aluco),
 European Nightjar (Caprimulgus europaeus),
 Black Woodpecker (Dryocopus martius),
 Green Woodpecker (Picus viridis),
 Goshawk (Accipiter gentilis),
 Golden Eagle (Aquilla chrysaetos),
 Eastern Hedgehog (Erinaceus concolor),
 Red Squirrel (Sciurus vulgaria),
 Common Dormouse (Muscardinus avellanarius),
 Forest Dormouse (Dryomys nitedula),
 Edible Dormouse (Glis glis),
 Brown Hare (Lepus europaeus),
 Beech Marten (Martes foina),
 Badger (Meles meles),
 Red Fox (Vulpes vulpes),
 Wildcat (Felis silvestris),
 Balkan Lynx (Lynx lynx martinoi).
 Wolf (Canis lupus),
 Brown Bear (Ursus arctos),
 Wild Boar (Sus scrofa),
 Red Deer (Cervus elaphus) and
 Roe Deer (Capreolus capreolus).