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Currently, there is an increasing need for evidence-based strategies in nature conservation, for example when designing and establishing nature reserves. In this contribution, we critically assess the ecological relevance of recent nature conservation practices in Kenya (East Africa), a region of global biodiversity hotspots. More specifically, we overlay the distribution of species richness (here based on mammals, birds, amphibians and vascular plants) with the location of nature reserves, the Kenyan agro-ecological zones (areas representing diverging agricultural potentials), and with the spatial distribution of human population density. Our analyses indicate that the majority of protected areas are located in areas with comparatively low species richness, while areas with extraordinary high levels of species richness are not adequately covered by nature reserves. Areas of high agricultural productivity (and with high human demographic pressure) are mainly reserved for high-yield agriculture; however, these regions are also characterised by high species richness. The majority of nature reserves are restricted to the semi-arid regions of Kenya, marginal for agricultural usage, but also with low levels of species richness. Based on this analysis, we prioritize areas for future protection. This single-country case illustrates that agricultural production in high-yield areas outweighs nature conservation goals, even in global biodiversity hotspot regions, and that priority setting may conflict with effective nature conservation.