Lowlands (Terai and Siwalik Hills) – land below 1000 m, comprising 27% of Nepal's surface area. Below 500 m the vegetation is tropical, and between 500 and 1000 m it is subtropical. These lands are heavily populated and there are great pressures on forest resources. 1885 species of angiosperms, 81 species of pteridophytes, and 61 species of bryophytes have been recorded from the Lowlands ([BBP] 1995), but these areas are comparatively botanically poorly explored and the figures are certainly underestimates.

Mid-Hills (Mahabharat Lekh and Midlands) – land between 1000-3000 m, comprising 30% of the surface area of Nepal. Between 1000-2000 m the climate is monsoonal with warm temperate vegetation, at 2000-3000 m the vegetation becomes cool temperate. The Mid-hills have the greatest ecosystem diversity as well as species diversity in Nepal (see vegetation), and nearly 32% of forest cover occurs in this region. 33 of the 52 Mid-Hills ecosystems are represented in protected areas. Most of the botanical exploration in Nepal has been undertaken in the Mid-Hills, and 3364 species of angiosperms, 16 species of gymnosperms, 272 species of pteridophytes, and 493 species of bryophytes have been recorded ([BPP] 1995).

Highlands (Himalayan mountains, High Mountain Valleys, and Tibetan Marginal Mountains) – land above 3000 m, comprising 43% of the surface area of Nepal. Vegetation is sub-alpine between 3000-4000 m, alpine between 4000-5000 m, and tundra and arctic above 5000 m. Seven protected areas have been established in the Highlands, with another three spanning both the Mid-Hills and Highlands. These include 30 of the 38 Highlands ecosystems. The Highlands are less diverse than the lower zones, but are characterised by a higher number of endemic species. It is estimated that over 2000 angiosperms, 10 gymnosperms, 78 pteridophytes, and 347 bryophytes occur here.