Unlike the flora, the fauna in the National Park has been much less studied.  This statement especially applies to a large number of invertebrates.  They are present in large number with wide varieties on this mountain.  Vertebrates in the Park are better studied and listed.  In the National Park there are 171 species of vertebrates, fishes excluded, 10 amphibian, 18 reptiles, 124 birds, and 19 mammals.

It is worth mentioning the presence of chamois, lynx and bear, - mammals that are becoming rare in the rest of Europe, and the birds large and small cormorant and pelican that naturally live at Lake Prespa and island of Golem grad.

More elaborate studies are conducted at the water system at St Naum monastery, and there have been found some rare species.

At the moment, complete data about the wellbeing and size of population for the more significant species in the GNP, does not exist.  General conclusion is that they are in good condition.  Exemption to this statement is the Balkan lynx.  After 20 of absence, it has been spoted again in the area, but iths number are well under the biological capacity of the area.  Furthermore, there are indications for some species of birds that their numbers are significantly lower compared to previous period.  This especially applies to the birds of pray and for the vultures, and the reason is drastically decreased numbers of livestock on the area.