Background and aims - Plants are often overlooked in conservation planning, yet they are the foundation of all terrestrial ecosystems. The East Africa region is used to investigate the effectiveness of protected areas for conserving plants. With a wide range of ecosystems and 771 protected areas covering nearly one quarter of the land area, East Africa is an ideal location to assess the effectiveness of protected areas through distribution modelling of the genus Acacia. Methods - Herbarium specimen data (2,047 records) were collated from East Africa for 65 taxa (species, subspecies, varieties) from the genus Acacia. Generalised Additive Models were used to determine climatic drivers, and thence to extrapolate climatic suitability across the region. For two Acacia taxa, we investigated the potential for climate-induced range-shifts using a downscaled regional climate model under two IPCC scenarios. Key results - Approximately two thirds of Acacia diversity hotspots had < 10% coverage by protected areas. Furthermore, the protected area network covered less of the predicted ranges of the Acacia taxa and contained fewer taxa per unit area than would be expected under randomised placement. Areas with suitable climate for high-elevation, moisture-dependent taxa such as A. abyssinica subsp. calophylla are predicted to contract their potential range by up to 80% towards mountain peaks, where protected areas are dominated by low-level protection forest reserves. Conversely, the area of suitable environment for a xerophytic low-elevation species (A. turnbulliana) is predicted to increase by up to 77%. Conclusions - East Africa's national parks may not be preserving an important component of ecosystem diversity, a situation exacerbated by climate change. Even within the genus Acacia, different species are predicted to respond differently to climate change. Priority areas for research and conservation are identified based on overlap between predicted high Acacia diversity and gaps in the collection record, with northern and eastern Kenya highlighted as particularly important. High elevation protected areas are also predicted to become increasingly important as climatic refugia in a warmer future. © 2012 National Botanic Garden of Belgium and Royal Botanical Society of Belgium.