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The ecoregion hosts a very high faunal diversity, mainly with regard to birds. The ecoregion includes many IBAs (Important Bird Areas) as well as threatened SPECs (Species of European Concern). Mountain lakes (i.e. the Prespa Lakes) host an amazing bird fauna. These include large breeding colonies of herons, spoonbills, and egrets, as well as two pelican species. The Dalmatian pelican population of Prespa represents one of the few colonies in Europe. 

The brown bear (Ursus arctos) population is still significant and under threat. Wolf (Canis lupus) and jackal (Canis aureus) are also two important endangered large mammals from the ecoregion. 

Other large mammals that live in the park are lynxes, deers and wild cats, with the last two being found in the area of Flegga forest. Additionally wolves, beech martens, wild boars and red squirrels are present in the area all year round. On the other hand, the Balkan chamois, a Balkan endemic species, is found on the steep and rocky parts of the park, as well as in areas with beech forests. Its population density fluctuates between 3-5 and even 20 individuals per 100 ha (250 acres) depending on the habitat productivity. The three small rivers crossing the area of the park have very clear water and are the well conserved habitat of the otter.

In the area of the national park up to five types of bat have been reported, with most common being niktovatis (Nyctalys noctula). Moreover, it provides shelter for than 80 species of birds, such as 10 types of rare bird species including the eastern imperial eagle, golden eagle, Levant sparrowhawk and the lanner falcon, which indicates the ornithological importance of the area. One of the rare birds found in the park is the shore lark (Eremophilla alpestris), found in the alpine meadows, and the great grey shrike (Lanius excubitor), which migrates in the summer from Africa. The dense and mature forests of the area host eight types of woodpecker, including the white-backed, the middle spotted, the lesser spotted and the black woodpecker.

In total, 415 types of plants and 86 species of mushroom are recorded in the area. A number of local flower types are considered endemic to the Balkans, such as Dianthus deltoides and Allium breviradum. On the other hand, many endemic plants of central and northern Greece grow also in the park, like the Centaurea vlachorum. Moreover, rare species of the forests of Pindus mountains, typical of the lower geological layers, are Minuartia baldaci, Bornmuellera tymphaea, Campanula hawkinsiana, Viola dukadjinica and Silene pindicola.^[6] The most important places for the gathering of rare plants are the northern slopes of the peaks of Aftia, Flegga and Kapetan Kleidi. All the above places are very steep and difficult for grazing animals and therefore natural regeneration of the forest in this area is progressing normally and many rare plants are conserved. The serpentine soil, which is dominant in the area of the Pindus National Park also favors the growing of rare endemic plant species.