Prespa National Park is worldwide recognized for the presence of endemic fishes with a number of 6 species such as the Prespa barbell (Barbus prespensis), the Prespa nose (Chondrostoma nasus prespensis), and others.
In Prepsa are found the common mountain carnivores and herbivores that occur in Albania such as the brown bear (Ursus arctos), grey wolf (Canis lupus), wild boar (Sus scrofa), roe dear (Capreolus capreolus), etc. Here is also commonly found the European otter (Lutra lutra).
Avifauna of the area is rich and Prespa is recognized internationally as an Important Bird Area. Here is the only site in Albania where both species of Pelicans (Pelecanus crispus and Pelecanus onocrotalus) are commonly seen together. In addition, due to the high diversity of habitats: land, forest and alpine pasture species many other species of birds occur in the area. We may highlight here the Blue-rock Thrush (Monticola solitaries), the Rock Nuthatch (Monticola saxatilis), the Rock Partridge (Alectoris graeca), the Horned Lark (Eremophila alpestris), and many other species.
The site is very interesting when it comes to the herpetofauna as here it is the only place in Albania where the Greek Tortoise or the Spur-thighed Tortoise (Testuda greaca) occurs. In addition, another very interesting spot is also the Maligradi Island or Snake Island, containing a high breeding density of both water snakes: Grass Snake (Natrix natrix) and Dice Snake (Natrix testellata). The presence of lizard species is also quite dense in the island.
Ohrid Lake holds more or less the same fauna composition as the Prespa Lakes, nevertheless is less rich in terms of avifauna. The area is known though for several endemic fish species such as the Ohrid Trout (Salmo trota ohridanus) etc.