An objective process of biodiversity zoning is presented using the Greater Fish River Canyon Landscape in southern Namibia (partially overlapping with the Ai-Ais - Richtersveld Transfrontier Park, which stretches across both sides of the Orange River) as an example. Using satellite imagery, broad habitat units were mapped, and plant species lists were compiled for these units, based on local, national and regional distribution data, published information and targeted field work. Formal protection, redlist status, and an index of rarity based on distribution range and endemism were used to determine a rating for species of conservation importance. These ratings were summed per landscape unit, providing an overall rating for each unit. The topographically heterogeneous landscape in a transitional area between southern Africa's winter and summer rainfall regimes was delineated in 32 landscape units. A total of 835 plant species was included in this study, 265 of which were defined as having particular conservation importance. The systematic incorporation of level of endemism and an index of rarity based on range size, facilitated a fully objective process of biodiversity zoning. The resulting zoning presents a relative measure of prioritisation for conservation, sufficiently flexible to be adapted to the species richness and data range in a particular study area and is therefore site-specific. Although a large part of the study area is formally protected in state-protected areas and adjoining private nature reserves, nearly 50% of the most important area in the western Succulent Karoo section of the landscape is on private farmland and townlands of the mining town Rosh Pinah with no formal protection. Also, exploration and small-scale mining take place along the Orange River. All these factors pose a threat to some of the rarer plants. Keywords: biodiversity, endemism, zonation, Gariep, mountain flora, rarity, range size, Succulent Karoo biome, transfrontier park, Namibia, Fish River Canyon.