An understanding of rarity and how it relates to extinction risk is a central concern of conservation biology. Classic conceptions of rarity revolve around spatial rarity, based on distribution and abundance, rather than temporal rarity, where species may be common following certain conditions but rare for most of the time. This form of rarity is likely to be especially prevalent in highly variable arid systems. Rarity in the arid zone is also characterised by poorly understood threats, such as grazing, and may also reflect low collection effort given the vast and inaccessible areas involved. This study explores rarity and threat in the arid zone, based on the flora of a large region of western Queensland. The status of all species known to occur in the study area was systematically assessed, and the current list of threatened species was examined for bias in forms of rarity, life forms and habitats. Five threat syndromes were identified, arising from the interaction of plant biology and threatening processes. Over 60 potentially threatened species have been overlooked in the listing process. The list is dominated by narrow endemics from residual and spring habitats and the species from springs at least are genuinely threatened. Widespread but sparsely occurring species are under-represented in the current list, as are grasses. With the exception of spring-dependent species, plant conservation in western Queensland is currently constrained by lack of basic data on distribution, abundance, population dynamics and realistic threat syndromes for nearly all species. Separating the influence of genuine rarity, temporal rarity and low collection effort, as well as a more detailed understanding of threatening processes are needed to address plant conservation in the arid zone.