In the present thesis molecular methods are used to study phylogeny and phylogeography of the Central European caddisfly Rhyacophila pubescens, an aquatic insect which shows an insular distribution pattern due to a geological factor. The species is restricted to tufa streams which only occur in limestone mountain areas. The first chapter serves to study monophyly of R. pubescens individuals obtained from different areas of the distribution range using two mitochondrial (mtCOI, mtLSU) and one nuclear (nuWG) marker. Additionally monophyly of the R. tristis-group was analysed using a subset of species. Monophyly of R. pubescens and the R. tristis-group specimens were confirmed. In the second chapter the genetic population structure of the former periglacial area north of the Alps is analysed using a sequence fragment of mtCOI of 197 R. pubescens individuals from 33 sites. Results show that the area was most probably recolonized after the last glacial maximum due to the shallow structure of the haplotype network. A high degree of differentiation at the stream level suggests that gene flow between populations in suitable habitat areas is low, illustrating the habitat specificity of the species. In the third chapter the phylogeography of the entire range of R. pubescens is studied using mtCOI- sequence data and Amplified Fragment Lengths Polymorphisms. Both markers show higher genetic diversity in Southern Europe and genetic impoverishment of the northern part of the range consistent with rapid colonization of this area after the last ice age. Inter alia, migration rates indicate that the refugial region is located in the Dauphiné Alps. The data allow to infer a recolonization route along the Western Alps to the area north of the Alps, which is for the first time shown for an aquatic invertebrate.