Much of the territory is untouched by human activity and so supports Ice Age relict floral communities through all altitude zones - pine and birch forest, dark coniferous taiga, alpine meadows and mountain tundra.

Ziglalga National Park connects two large protected areas on the main ridge of the Southern Urals, with Zyuratkul National Park to the northeast, and the South Ural Nature Reserve to the southwest.

The highest point is at Mount Poperechnaya (1,387 metres (4,551 ft))[3] The park is at the southern extremity of the Urals montane tundra and taiga ecoregion.

It is closely surrounded on three sides by three other ecoregions: East European forest steppe to the west, West Siberian taiga to the northeast, and Kazakh forest steppe to the south.

Alpine peat bogs are common, both mesotrophic and oligomesotrophic, as are a number of boreal plant species at the southern end of their range.