There are nine nature reserves within the 'Central Balkan' National Park, accounting for about 28% of its total area:
- 'Boatin' Nature Reserve (1,597.2 hectares)
- 'Tsarichina' Nature Reserve (3,418.7 hectares)
- 'Kozya Stena' Nature Reserve (904.3 hectares)
- 'Steneto' Nature Reserve (3,578.8 hectares)
- 'Stara Reka' Nature Reserve (1 974.7 hectares)
- 'Dzhendema' Nature Reserve (4,220.2 hectares)
- 'Severen Dzhendem' Nature Reserve (1,610 hectares)
- 'Peeshtite Skali' Nature Reserve (1,465.7 hectares)
- 'Sokolna' Nature Reserve (1,250 hectares)
The 'Boatin' Nature Reserve, 'Tsarichina' Nature Reserve, 'Steneto' Nature Reserve and 'Dzhendema' Nature Reserve have all been designated as UNESCO Biosphere Reserves.
The flora of the 'Central Balkan' National Park is extremely rich, some 1900 species and sub-species of higher plants which represents about half the Bulgarian flora. These include 10 local endemics (found nowhere else in the world), 10 Bulgarian endemics (known only from Bulgaria) and 67 Balkan endemics (growing only on the Balkan Peninsula).
The 'Central Balkan' National Park also has an extremely varied fauna. The invertebrate fauna is still only partly studied, but already over 2300 species and subspecies have been recorded. These include 9 species of dragonfly (Odonata) and many interesting butterflies (Lepidoptera).
The vertebrate fauna of the 'Central Balkan' National Park has been studied in much greater detail, and includes 6 species of fish, 8 species of amphibians and 14 species of reptiles. Some 224 species of birds have been recorded within the national park itself, of which 123 species have been recorded as breeding. This number increases to 151 nesting species if one includes the species that have been recorded breeding in adjacent areas and which fall within the 'Central Balkan' Important Bird Area (IBA). Some 59 species of mammals have been recorded in the 'Central Balkan' National Park. These include 18 species of bats, 25 species of small mammals (insectivores and rodents), and 16 species of large mammals, of which 12 species are carnivores including brown bear, wolf, jackal and even a record of a lynx.