Freshwater biodiversity has shown to be highly vulnerable to climate warming, alpine cold stenotherm populations being especially at risk of getting extinct. This paper aims at identifying the environmental factors favouring cold stenotherm species in alpine ponds. This information is required to provide management recommendations for habitats restoration or creation, needed for the mitigation of the effects of climate warming on alpine freshwater biodiversity. Cold stenotherm species richness as well as total (i.e. stenotherm and eurytherm) richness were analyzed for aquatic plants, Coleoptera and Odonata in 26 subalpine and alpine ponds from Switzerland and were related to environmental factors ecologically relevant for pond biodiversity. Our results confirmed that the set of environmental variables governing pond biodiversity in alpine or subalpine ponds is specific to altitude. Altitude and macrophyte presence were important drivers of cold stenotherm and total species richness, whereas connectivity did not show any significant relation. Therefore, the management of pond biodiversity has to be ‘altitude-specific’. Nevertheless, cold stenotherm species from the investigated alpine ponds do not show some specific requirements if compared to the other species inhabiting these ponds. Therefore, both total and cold stenotherm species richness could be favoured by the same management measures.