Although many species have similar total distributional ranges, they might be restricted to very different habitats and might have different phylogeographical histories. In the European Alps, our excellent knowledge of the evolutionary history of silicate-dwelling (silicicole) plants is contrasted by a virtual lack of data from limestone-dwelling (calcicole) plants. These two categories exhibit fundamentally different distribution patterns within the Alps and are expected to differ strongly with respect to their glacial history. The calcicole Ranunculus alpestris group comprises three diploid species of alpine habitats. Ranunculus alpestris s. str. is distributed over the southern European mountain system, while R. bilobus and R. traunfellneri are southern Alpine narrow endemics. To explore their phylogenetic relationships and phylogeographical history, we investigated the correlation between information given by nuclear and chloroplast DNA data. Analyses of amplified fragment length polymorphism fingerprints and matK sequences gave incongruent results, indicative for reticulate evolution. Our data highlight historical episodes of range fragmentation and expansion, occasional long-distance dispersal and on-going gene flow as important processes shaping the genetic structure of the group. Genetic divergence, expressed as a rarity index (‘frequency-down-weighted marker values’) seems a better indicator of historical processes than patterns of genetic diversity, which rather mirror contemporary processes as connectivity of populations and population sizes. Three phylogeographical subgroups have been found within the R. alpestris group, neither following taxonomy nor geography. Genetic heterogeneity in the Southern Alps contrasts with Northern Alpine uniformity. The Carpathians have been stepwise-colonised from the Eastern Alpine lineage, resulting in a marked diversity loss in the Southern Carpathians. The main divergence within the group, separating the ancestor of the two endemic species from R. alpestris s. str., predates the Quaternary. Therefore, range shifts produced by palaeoclimatic oscillations seem to have acted on the genetic structure of R. alpestris group on a more regional level, e.g. triggering an allopatric separation of R. traunfellneri from R. bilobus.