There are four nature reserves within the 'Rila' National Park, accounting for about 20% of its total area:
- 'Parangalitsa' Nature Reserve (1,509 hectares)
- 'Skakavitsa' Nature Reserve (70.8 hectares)
- 'Ibar' Nature Reserve (2,248.6 hectares)
- 'Central Rila' Nature Reserve (12,393.7 hectares)
The flora of the 'Rila' National Park is exceptionally rich, some 1400 species of higher plants which represents nearly 40% of the total number of species found within Bulgaria. These include 3 local Rila endemics (found nowhere else in the world), 18 Bulgarian endemics (known only from Bulgaria) and 36 Balkan endemics (growing only on the Balkan Peninsula).
The 'Rila' National Park also has an extremely diverse and interesting fauna. The invertebrate fauna is still only partly studied, but already almost 3000 species have been found, and the final total is estimated to be around 7000 species. These include several interesting species of dragonfly (Odonata) and butterflies (Lepidoptera).
The vertebrate fauna of the 'Rila' National Park has been studied in more detail, and includes 12 species of fish, 10 species of amphibians and 10 species of reptiles. Some 99 species of birds have been recorded breeding within the national park itself, but this number increases to 130 species if one includes the species that have been recorded breeding in adjacent areas and which fall within the 'Rila' Important Bird Area (IBA). Some 49 species of mammals have been recorded in the 'Rila' National Park. These include 10 species of bats, 23 species of small mammals (insectivores and rodents), and 16 species of large mammals, of which 11 species are carnivores including brown bear and wolf.