ABSTRACT Spatial conservation tools usually focus on identifying areas having species groups of interest. Consequently, there is a need to identify the main factors influencing the concentration of species (hotspots) and their locations. We asked: whether existing strictly protected areas are efficient to cover the main regional biodiversity hotspots; what characteristics are associated with hotspot arrangement; what is the minimal distance from a biodiversity research center needed to cover the main biodiversity amount. We analyzed factors influencing the spatial arrangement of 164 threatened plant species in the Republic of Mordovia (European Russia). To quantify species distribution, we used a grid mapping approach using 100 km2 quadrats. We identified four biodiversity research centers (BDRC) of threatened plant species in the study area, including two protected areas, the town of Saransk, and a regional key conservation area. About 50% of species and species locations were concentrated within a 24-km radius around BDRCs. From our results, buffer zones of protected areas should have a 5–10 km width and the establishment of new protected areas should be preceded by the identification of regional biodiversity hotspots. Additionally, the correctness of protected area arrangement with plant species richness in a region should be tested.