Pirin offers unique high-mountain scenic landscape at the cross-road between the central European, Mediterranean and Ponitic biogeographical regions.

The uniqueness of Pirin ensues from its relative isolation from the other mountain chains. Compared with them the Mediterranean influence, penetrating along the river valleys of Struma and Mesta Rivers, here is stronger. This results in the unique combination of the widespread Mediterranean species (12%) and the much less represented Arctic-Alpine species (less than 1%), although the relief of the mountain is a typical Alpine one.

Exceptional biological diversity and high percent of the endemic component characterize Pirin. Pirin endemic species are fourteen higher plants, which is more than half of all the Bulgarian endemic plants:

- 17 higher plants and two animals are Bulgarian endemic species;

- 86 higher plants and 6 representatives of the vertebrate fauna are Balkan endemic species.

Despite the fact that only two groups of invertebrates have been studied in Pirin – Arthropods and Mollusks, the richness of the invertebrate fauna is indisputable: 216 endemics and 176 relicts.

One of the greatest riches of Pirin is its forest. Forest of natural character, aging over 140 years, and covers more than half of the territory of the protected area. More than 90% of the forests are coniferous, and the occurrence of the two endemic species – Macedonian pine (Pinus peuce) and Bosnian pine (Pinus heldreichii) – diversifies this clearly differentiated coniferous belt.

Of all the habitats described on the territory of Pirin, the rock habitat is the most representative for the unique character of the mountain. Refuges of the unique rock flora and fauna are the 35 cirque valleys, the 180 glacial lakes, the pyramidal and conic summits and the picturesque rock phenomena.

The identification of Pirin NP as a CORINE Site in 1998 confirmed its value as a key territory of a high conservation importance. Because of the priority habitats and species occurring in Pirin, the site has also been proposed to become a Natura 2000 site. Pirin has been designated an Important Bird Area that will allow the long-term preservation of threatened bird species in their natural habitats.

The Pirin NP has been inscribed as one of the 114 Important Plant Areas of Bulgaria under the criteria of occurrence of threatened species, threatened habitats and floral richness.