Montane vegetation has been likened to islands in a sea of savanna woodland. There are a number of plant species restricted to, or endemic to certain mountains, such as the Nyika Plateau and Mount Mulanje in Malawi. Many of these species are grassland herbs, and are not normally woody plants. The fynbos-like shrublands on the highest plateaux in the Nyanga area in Zimbabwe have similarities with the fynbos of the Cape, although they do not have the same level of species diversity.

Species found in the Montane biome are generally restricted to these habitats. Rainforest is found only where local climatic conditions allow it to develop such as in sheltered gullies or on the gentle windward slopes of mountains. Rainforests are rich in plant diversity, and because so much of the original forest extent has been cleared for agriculture, they are of major conservation interest.

Most of the broad seasonal rivers have a fringe of large trees such as Winter thorn, Natal mahogany, Acacia and Waterberry, but in many places these fringes are being destroyed by clearance for agriculture or woodfuel. Riparian fringes are an important wildlife habitat and corridor. They also protect riverbanks from erosion.

At the headwaters of the Zambezi in Mwinilunga district of Zambia and in northeastern Angola, the gallery or riverine forests have a different species composition to those further downstream, with species more typical of the Congo Basin. These species are of great conservation interest from a basin-wide perspective as they are so limited in occurrence here. The different species composition of this area is also mirrored in the biodiversity of other groups such as birds, small mammals, dragonflies and butterflies.

At the mouth of the Zambezi and along tidal creeks are mangrove swamps comprising specialised trees such as Red and White mangroves, which are of significant biodiversity interest. Mangroves are not speciesrich due to the high level of adaptation required to a saline environment.