Many studies have highlighted the importance of mountain ecosystems as hotspots of biodiversity and endemism. In this study, we used biogeographic partitioning to explore the diversity patterns of high-mountain flora in south-western Europe by analysing the richness of the main floristic elements in relation to geographical and ecological factors (climate, isolation, elevation, etc.). Taxa that inhabit above 1600 m a.s.l. in the Iberian Peninsula were selected using bibliographic sources. Hierarchical agglomerative clustering and non-metric multidimensional scaling (NMDS) were used to explore the patterns of taxonomic diversity across the main biogeographic elements. Six environmental variables were calculated to account for inter-range variation in species richness and biogeographic elements. The results showed that at a broad scale, the main floristic elements correlated with specific eco-geographical factors. The Arctic–Boreal element was strongly, negatively correlated with summer drought and showed a higher taxonomic distinctness than expected. The Iberian endemic element was related to isolation and maximum elevation and although it was the richest element, it demonstrated a relatively low taxonomic diversity, in particular in the Baetic Range. Biogeographic origin is an important driver of the diversity patterns of high-mountain flora. In the Iberian Peninsula, these patterns show a North–South gradient, which reflects historical processes of migration and speciation that were constrained by climatic fluctuations during the Ice Ages. Although species richness is the usual biodiversity measure considered in conservation strategies, the use of taxonomically related indices helps to understand better the general diversity patterns and to better document strategies of biodiversity conservation.