AbstractThis paper presents a perspective of how phylogenetic and phylogeographic hypotheses, based on nuclear DNA sequence variation (ITS) or amplified fragment length polymorphisms (AFLPs), can provide insights into the origin and evolution of the European high mountain flora. We focus on a diversity of unrelated herbaceous plant taxa that are broadly co‐distributed across the European Alpine System, representing different taxonomic levels, and having either Mediterranean or Asian affinities (i.e.,Anthyllis montana, Pritzelago alpina, Globulariavs.Soldanella, andPrimulasect.Auricula). Our observations highlight that all taxa investigated began to diversify at the beginning of the Pleistocene or well within this period. Some of those taxa apparently followed different routes and modes of immigration, thereby colonizing the European high mountains only once (either from the East or the West) or repeatedly (from the Mediterranean Basin). Our observations further suggest that several high mountain taxa originated from lowland forms. While supporting earlier views, such a trend has generally been associated with pre‐Quaternary rather than Pleistocene events. While several concordant patterns of (large‐scale) spatial genetic differentiation are identified across taxa, such similarities may have arisen at either clearly different or roughly similar times. Finally, most speciation events likely occurred in allopatry, though more comprehensive studies are required to evaluate the relative importance of non‐allopatric modes of speciation in the study area. We conclude that one major challenge to future evolutionary studies in European mountain plants is the accurate and reliable reconstruction of the tempo and mode of speciation across Quaternary time scales.