As part of the Mountain Baba, it is located between the ravines Prespa and Pelagonia. It is over 2000m above sea level high, and it has another 24 mountain peaks. The ambient values of the park are intensified with the mountain rivers Sapuncica, Semnica, Crvena Reka, Sara, Brajcinska Reka etc. that have preserved their natural beauty. Their waters are clean and rich with trout.

The Molika in the Republic of Macedonia is one of the two autochthon pines in Europe. The Molika forests on Pelister are mainly concentrated between 1200 and 2100 metres above sea level, although individual samples and groups can be found below 1000 metres. There are 1.092ha of pure Molika forests on Pelister, while 477ha are mixed with fir trees, and 110 ha with oak trees.

The irrigation zone is spread out on an area of about 3.000 ha, the tourist zone is 2.500 ha, the strictly protected areas are predominant, with an area of 3.637 ha. Several natural rarities are within the strictly protected zones, whereas some parts with Pelister pine, mountain alp vegetation, geomorphological forms etc. are special areas. Another important feature is the oak i.e. fir forests that have highland pastures within the national park.21 vegetation communities are registered in Pelister 10 of which are forest vegetation and the rest are grass.

Wild life in Pelister is present with 44 species or 42.7% from the total number of wild life in the Republic of Macedonia. 14 species or 45.2% is permenently protected wild life, while 13 species or 76.5% is with no legal protection.