Phylogenetic patterns, adaptations and conservation status of the rare species flora of a winter-summer rainfall ecotone in southern Africa were investigated to shed light on the species' evolutionary history and conservation requirements. Some 11% (93 species) of the Greater Fish River Canyon Landscape in Namibia were classified as rare species, more than half currently not receiving formal protection in Namibia. The rare species flora does not present a subset of the overall species pool, but a unique assemblage of plant species, over-represented by members of the family Mesembryanthemaceae, Crassulaceae, Asphodelaceae and Hyacinthaceae. Low growth forms (dwarf leaf-succulent shrubs, dwarf stem succulents and dwarf deciduous shrubs) as well as bulbs are more common amongst rare species. Multiple factors and processes, likely interlinked, are believed to be responsible for determining the rare species flora, indicating that individual species respond differently to the challenges posed by this arid environment. Some plants are likely remnants of wetter conditions in the past, which have retained viable populations in the mountainous terrain of this landscape, others may have evolved in situ.