Rila National Park boasts four nature Reserves within its province: Parangalitsa, Central Rila Reserve, Ibar, and Skakavitsa.

These four Reserves have a combined area of 16,222.1 hectares, of which 16,132.7 hectares are forested, and the remaining 89.4 hectares include high mountain meadows and pastures. The four Reserves occupy 20% of the Park. Each Reserve has biotic complexes of extremely high conservation significance. The Parangalitsa Reserve and parts of the Central Rila Reserve are included on the UNESCO List of Biospheric Reserves under the Man and Biosphere Program.

Parangalitsa, declared back in 1933, is the second oldest Bulgarian reserve—just one day younger than Sylcosia. Its name is derived from the Greek parangalos, meaning ‘forbidden,’ or ‘off limits.’ The Reserve occupies part of the southwestern slopes of Rila Mountain, covering 1,509 hectares. It contains some of the oldest spruce forests in Europe—the average age of individual specimens is 200 years or older. The forests provide favorable habitats for the 290 higher plants and numerous animal species protected by law and listed in the Red Data Book of Bulgaria. Parangalitsa Reserve has been listed on the UNESCO List of Biospheric Reserves under the Man and Biosphere Program since March 1977.

The Central Rila Reserve is the largest in Bulgaria and one of the largest in Europe. It was established in 1992 to conserve forest, sub-alpine, and alpine ecosystems that form a unique natural complex. The Reserve sets the example for proper biodiversity conservation in the mountains of Central and Southern Europe. With a total area of 12,393.7 hectares, it encompasses a considerable amount of territory around Mussala with a markedly alpine terrain: jagged rocky ridges, screes, and cornices. Human impact on the coniferous forests of spruce and white fir of the Reserve is minimal, less than anywhere else in Bulgaria. The sub-alpine zone is dominated by dwarf pine shrubbery.

Unique flora and fauna of relict (surviving from previous geological ages) and endemic (limited in area) species characterize Central Rila Reserve. There are numerous populations of Rila cowslip, spotted gentian, spring pasque flower, Bulgarian avens, and the snow-edge bell. Rhododendron myrtifolium, one of the few evergreen plant species in Bulgaria, grows on the northern slopes, at altitudes above 2,000 meters. Central Rila Reserve is home to the largest Balkan chamois herd in Bulgaria. Other permanent inhabitants include bears, martens, capercaillia, hazel hens, and black woodpeckers.

Another strictly protected area, Marichini Ezera, is incorporated within Central Rila Reserve, and retains its status as a Biospheric Reserve.

Ibar was set aside as nature Reserve in 1985 to protect the dwarf-pine shrubbery forests as well as locations of relict plants and rare animal species. With an area of 2,248.6 hectares, it lies on the high slopes north of the main mountain ridge, between Ibar and Belmeken peaks. The extreme variations in altitudes determine the exceptionally high biological diversity within its territory. Over 400 species of higher plants have been identified, including the Rila cowslip, Transylvanian campanula, and many others. The fauna is no less diverse, the Reserve is home to no fewer than 50 species of birds, some of which—the golden eagle and large hawk—are threatened with extinction. Others, like shore lark and alpine accentor, are glacial relicts or Balkan-endemic subspecies. Glacial relicts have also been identified among the reptiles, amphibians, and mammals. Large mammals include bears, wolves, roe, foxes, and wild boar. The Reserve is also home to a locally endemic species of souslik.

Skakavitsa is one of the smaller Bulgarian Reserves, with a territory of a mere 70.8 hectares. Designated in 1968, it is located in the northwestern section of the Rila Mountains at altitudes between 1,850 and 2,050 meters above sea level. This is a typical forest Reserve, designed to protect ancient white fir forests. Among the protected plant species are globeflower, Bulgarian avens, golden columbine, roseroot. Common valerian and yellow gallium are two of the rare plant species that reside in Skakavitsa Reserve. The roe, wild boar, fox, wolf, capercaillie, black woodpecker, nutcracker, viper, and the common frog are representative of the Reserve’s fauna.