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In mountain regions, climate change is resulting in glacial retreat, causing biodiversity loss in glacial‐fed streams (kryal habitat). Diamesa species (Diptera Chironomidae), the main colonizers of the kryal in the Alps, are the aquatic insects more threatened by extinction. In recent years, DNA barcoding was successfully adopted to delimit species of chironomids and provided species identification. We highlighted that for the Diamesa genus, inconsistencies remain between identification on a morphological and molecular basis, mainly within cinerella and zernyi groups, raising doubts about the validity of head colour as a good diagnostic taxonomic character. Molecular phylogeny reconstruction based on mitochondrial (cytochrome oxidase subunits I and II) and one nuclear (ribosomal 18S rRNA) markers revealed that D. bohemani and D. zernyi on one hand, and D. cinerella and D. tonsa on the other hand, represent populations of the same species. Divergence times suggested that the radiation of these alpine species seems to have been driven by the climatic events with the alternation of glacial periods that happened in the Pliocene and Pleistocene. The initial separation of the oriental species D. steinboecki seems to be due to the tectonic movements of the Periadriatic fault system that probably favoured the emergence of lakes and streams, successively colonized by D. steinboecki. This study raises important concerns, from the validity of diagnostic characters used today to identify larval types up to the uncertainty about how many species of Diamesa inhabit the European Alps and what their fate will be within the scenario of climate change. [ABSTRACT FROM AUTHOR]