Increasing conflicts and social insecurity are expected to accelerate biodiversity decline and escalate illegal wildlife killing. Sahara‐Sahel megafauna has experienced recent continuous decline due to unsustainable hunting pressure. Here, we provide the best available data on distribution and population trends of threatened, large vertebrates, to illustrate how escalating regional conflict (565% growth since 2011) is hastening population decline in areas that were formerly refugia for megafauna. Without conservation action, the unique and iconic biodiversity of Earth's largest desert will be forever lost. We recommend: (1) establishing strong commitments for change in global attitude toward nature; (2) engraining a culture of environmental responsibility among all stakeholders; (3) fostering environmental awareness to drive societal change; (4) reinforcing regional security and firearms control; and (5) implementing local research and wildlife monitoring schemes. We identify relevant international partners needed to tackle these challenges and to make strong policy change for biodiversity conservation and regional stability.

Aim: Identification of priority conservation areas and evaluation of coverage of the current protected areas are urgently needed to halt the biodiversity loss. Identifying regions combining similar environmental traits (climate regions) and species assemblages (biogroups) is needed for conserving the biodiversity patterns and processes. We identify climate regions and biogroups and map species diversity across the Sahara‐Sahel, a large geographical area that exhibits wide environmental heterogeneity and multiple species groups with distinct biogeographical affinities, and evaluate the coverage level of current network of protected areas for biodiversity conservation.Location: Sahara‐Sahel, Africa.Methods: We use spatially explicit climate data with the principal component analysis and model‐based clustering techniques to identify climate regions. We use distributions of 1147 terrestrial vertebrates (and of 125 Sahara‐Sahel endemics) and apply distance clustering methods to identify biogroups for both species groups. We apply reserve selection algorithms targeting 17% of species distribution, climate regions and biogroups to identify priority areas and gap analysis to assess their representation within the current protected areas.Results: Seven climate regions were identified, mostly arranged as latitudinal belts. Concentrations of high species richness were found in the Sahel, but the central Sahara gathers most endemic and threatened species. Ten biogroups (five for endemics) were identified. A wide range of biogroups tend to overlap in specific climate regions. Identified priority areas are inadequately represented in protected areas, and six new top conservation areas are needed to achieve conservation targets.Main conclusions: Biodiversity distribution in Sahara‐Sahel is spatially structured and apparently related to environmental variation. Although the majority of priority conservation areas are located outside the areas of intense human activities, many cross multiple political borders and require internationally coordinated efforts for implementation and management. Optimized biodiversity conservation solutions at regional scale are needed. Our work contradicts the general idea that deserts are uniform areas and provide options for the conservation of endangered species.