In terms of fauna, the Pieniny Mountains are the best studied area of Poland. The large number of species which occur here reflects the great variety of habitats. Pieniny NP has about 7,100 species, 25 of which were documented here for the first time. Species known or thought to occur in the Park amount to 13,000 – 15,000, constituting almost half the total known throughout the entire country of Poland.

Invertebrates – Pieniny National Park is home to a wonderful variety of invertebrate life. So far about 6,800 species are found here. While there have been many studies of park invertebrates, not enough information is known to indicate exactly how many species occur here; it is thought that the total number of invertebrates may be around 13,000 species (about half of the known total from the whole of Poland). Epilithic grasslands serve as excellent habitat for many interesting species. The easiest to spot are butterflies, e.g. Zygaena sp., Large Blues Maculinea spp., Swallowtail Papilio machaon, Papilio padalirius, Parnassius mnemozyne. The most valuable and rare is the Apollo Butterfly Parnassius apollo. Pieniny meadows provide ideal sites for a wide variety of insects. Some of them are very rare and in Poland occur only in the Pieniny Mountains.

In the Pieniny area, the Dunajec river provides habitat for 17 species of fish. The most common ones are Chondrostoma nasus, Common Barbel Barbus barbus, Chub Leuciscus cephalus and Grayling Thymallus thymallus. Unfortunately, nowadays, the Dunajec river is not good for salmonids. Species like River Trout Salmo trutta morpha fario, Danube Salmon Hucho hucho or Cottus poecilopus and Bull-head (also known as Miller’s-Thumb) Cottus gobio are very rare, and Salmon Salmo salar is not found at all. It is interesting to note that species which are characteristic for lowland rivers are becoming more common.

 Amphibians and reptiles - There are 10 amphibian species in Pieniny: Alpine Newt Triturus alpestris, Carpathian Newt - T. montandoni, Smooth Newt T. vulgaris, Crested Newt T. cristatus, Spotted Salamander Salamandra salamandra, Bombina variegata, European Toad Bufo bufo, Green Toad B. viridis and Common Frog Rana temporaria. Reptiles are represented by the Sand Lizard Lacerta agilis, Common Lizard L. vivipara, Slow-Worm Anguis fragilis, Grass-Snake Natrix natrix, Smooth Snake Coronella austriaca and Adder Vipera berus.
All the species mentioned above are under protection in Poland.

Bird life in Pieniny is quite rich due to highly varied habitats, forested areas and water reservoirs. Some 188 species of birds can be found of which approximately 125 breed here. One of the most interesting is the Wall Creeper Trichodroma muraria, a species which is very rare in Pieniny and nests on limestone rock walls. Inaccessible rock benches provide nest sites for Kestrels Falco tinnunculus, Ravens Corvus corax and occasionally Rock Thrushes Monticola saxatilis which are at their northernmost edge of range in Pieniny.
The forests are well populated with birds. The most noteworthy sightings include the Black Stork Ciconia nigra, Spotted Flycatcher Muscicapa striata, Hazel Grouse Tetrastes bonasia, Woodpeckers – Black Woodpecker Dryocopus martius and Three-toed Woodpecker Picoides tridactylus, Nutcracker Nucifraga caryocatactes, Ring Ouzel Turdus torquatus and Willow Tit Parus montanus.
Owls are represented by the Eagle Owl Bubo bubo, Long-eared Owl Asio otus, Tengmalm’s Owl Aegolius funereus, Tawny Owl Strix aluco, Little Owl Athene noctua and the smallest one which is very rare – Pygmy Owl Glaucidium passerinum.
The most common bird of prey is buzzard Buteo buteo. Golden Eagle doesn’t breed in Polish part of Pieniny, but it can be spotted occasionally flying over the mountains.
Open areas e.g. meadows, woodland glades and ploughed fields provide ideal nesting sites for Grey Partridge Perdix perdix, Common Quail Coturnix coturnix, Whitethroat Sylvia communis, Common Stonechat Saxicola torquata and Skylark Alauda arvensis.
Wet areas near the Dunajec river serve as a refuge for Corncrake Crex crex which makes its characteristic two-syllabic "krret-krret" sounds in summer time at sunset. Water habitats are prime and suitable for the Little Ringed Plover Charadrius dubius, Kingfisher Alcedo atthis, Bank Swallow Riparia riparia, Dipper Cinclus cinclus, Grey Wagtail Motacilla cinerea and some species of ducks. Black-headed Gulls Larus ridibundus and Common Terns Sterna hirundo can be seen more and more often.
Between ten and twenty bird species that occur in Pieniny are recognized as being endangered. It is necessary to point out that bird species which exist in Poland (with few exceptions) are under strict protection. The exceptions are game-birds, Magpie Pica pica, Crow Corvus corone, Rook Corvus frugilegus and Common Heron Ardea cinerea, but these receive temporary periodic protection during the breeding season.

Mammals are represented by 61 species. The most numerous are small rodents of which the most noteworthy is the Herb Field Mouse Apodemus microps. Amongst the insectivorous mammals, there is a well-established population of Common Shrew Sorex araneus; the Alpine Shrew S. alpinus is also numerous.
The Pieniny Mountains are home to 17 species of bats. Although recognized as an endangered species in Poland, Lesser Horseshoe Bats Rhinolophus hipposideros are rather common in Pieniny and the largest colony can be observed in Jaworki. Bat species living in the Slovak Pieniny include the Greater Horseshoe Bat Rhinolophus ferrumequinum and Geoffrey’s Bat Myotis emarginatus – which is regarded by scientists as being extremely endangered. Many people consider bats to be vermin but they are invaluable allies to humans as they feed on numerous insects including those that cause crop damage. One should remember that all the bat species which occur in Poland are under protection.
The wide variety of Pieniny animal life also includes large mammals. Their populations are restricted and numbers are low due to the compact area of the Pieniny range and surrounding built-up areas which make migration difficult. The rarest amongst them is the Wild Cat Felis silvestris and the latest reliable information about this species is unfortunately a dozen or so years old. The Lynx Felis lynx is also extremely rare - the Pieniny population is estimated at just a few individuals. Sightings of Badgers Meles taxus, Weasels Mustela nivalis, Pine Martens Martes martes and Foxes Vulpes vulpes have been reported from the whole Pieniny area. The Dunajec river valley provides ideal nesting sites for Otters Lutra lutra. The presence of Beavers Castor fiber is worth noting. Wolves Canis lupus can be seen occasionally in Pieniny when they come from the neighbouring Gorce mountain range; they prefer large and sparsely populated forest areas. It is particularly exciting that traces of visiting Brown Bears Ursus actos have been observed in Pieniny in recent years.  The most common large mammals are Roe-Deer Capreolus capreolus, Red Deer Cervus elaphus and Wild Boar Sus scrofa.