The distribution pattern of European montane and arctic-alpine species is of growing interest among biogeographers due to the arising variety of inferred demographic histories. In this project we used five caddisflies (Trichoptera), one mayfly (Ephemeroptera) and one stonefly (Plecoptera) as model species to investigate the European Pleistocene and Holocene history of stream-inhabiting montane and arcticalpine aquatic insects. The selected model species represent the most common distribution patterns among montane aquatic insects, and all of them have geographically isolated sky island populations. By studying mtCOI for all species and microsatellite or AFLP data for four species across their respective distribution ranges, we aimed to reveal general genetic consequences of geographic isolation between isolated populations of caddisflies, mayflies, and stoneflies. The genetic data sets suggest different phylogeographic histories of the study species despite the similarities of present day distribution patterns. Thus, we can reject our null hypothesis of limited and comparable patterns of population genetic structure among the species. Instead we found evidence that each species exhibited its unique pattern, independent of similar distribution patterns or relatedness. The observed differences between the recolonization of Fennoscandia by the two arctic-alpine species Arcynopteryx compacta (Plecoptera) and Ameletus inopinatus (Ephemeroptera) highlight the fact that species with similar present distribution patterns do not necessarily share the same evolutionary history. The same is true for the different patterns observed among the boreo-montane caddisflies Chaedopterygopsis maclachlani, Drusus discolor, D. romanicus and Hydropsyche tenuis. The underlying causes may be found in the biology of the species, particularly their realized dispersal capacity. By comparing life history strategies of different species it is possible to evaluate present distributions with regards to the restrictions set by evolutionary processes and present selective pressures. Climate change always has and will continue to impact species distributions. However, the anthropogenic influence causes such rapid climate warming in most parts of the world that many species might not be able to cope. Cold-water adapted aquatic invertebrates, such as the study species of this project, will be especially sensitive to global warming, and may be among the most threatened species because they may lose a large part of their range and also a high amount of their present-day genetic diversity. Preserving genetic diversity, as one crucial sublevel of biodiversity, is essential to the overall fitness of a species, because decreased genetic variability may reduce the ability of single populations to adapt to changing environments triggered by current global warming and may thus result in local extinctions. Conservation management practices have to take these future climate change conditions into account. For one study species (A. inopinatus) we exemplarily present genetic, climatic, and ecological data that was used to prioritize conservation efforts for cold-adapted freshwater insects. Future SDM projects major regional habitat loss for A. inopinatus, particularly in Central European mountain ranges. By relating these range shifts to the population genetic results, we identified conservation units primarily in Eastern Europe, that if preserved would maintain high levels of the present-day genetic diversity of A. inopinatus and continue to provide long-term suitable habitat under future climate warming scenarios. Overall, our results provide a next step in filling the knowledge gap regarding molecular studies of the cold-adapted montane invertebrate fauna. However, there is continued need to explore the phenomenon of montane and arctic-alpine disjunctions to help understand the processes of range expansion, regression, and lineage diversification in Europe’s high latitude and high altitude biota.