In this study we aimed at comparing invertebrate diversity of high altitude lakes and ponds along hierarchical spatial scales. We compared local, among-site, and regional diversity of benthic macro- invertebrates in 25 ponds and 34 lakes in the Tatra Mountains, central Europe. The ponds showed significantly lower local diversity, higher among- site diversity and similar regional diversity than the lakes. The species-area relationships (SAR), habitat heterogeneity, and environmental harshness are assumed as drivers for the local diversity patterns. An ecological threshold separating pond and lake systems emerged at an area of 2 ha, where the SAR pattern changed significantly. Differences in species turnover between these systems were likely driven by greater environmental variability and isolation of the ponds. High altitude ponds neither significantly sup- port greater regional diversity nor higher number of unique taxa than lakes. The higher among-site diver- sity of ponds relative to lakes highlights the relevance of ponds for regional diversity in mountain areas.