Harvestmen (Opiliones) are one of the oldest arachnid groups and their low dispersal capabilities make them highly rewarding study organisms for research on endemism and faunal history. The genus Megabunus (Eupnoi, Phalangiidae) includes eight described species in Europe, with five species restricted to the Alps. Rigorous species delimitation is a requirement for conservation management and biodiversity research, but defining species has been a much disputed subject, and detecting real species boundaries can be challenging. Integrative Taxonomy, a method that uses multiple independent lines of evidence, can help to precisely delimit species and to uncover processes behind speciation. In this project, multiple disciplines, including molecular, morphometric and chemical data were applied in a discovery approach to reassess species limits in the Alpine endemic Megabunus harvestmen. In more detail, for the nuclear molecular analyses, a 54-sequencing approach of reduced representation libraries allowed the development of cross-species amplifying primers; primer pairs for six anonymous nuclear loci were further used. Subsequently, the most reasonable species hypotheses were invoked, and the most plausible evolutionary scenarios were discussed. This project demonstrates the applicability of discovery-based approaches in combination with validation approaches in a difficult taxonomic group. As a result, nomenclatural consequences could be implemented for the genus, three morphologically diagnosable new species (M. cryptobergomas Muster & Wachter, 2015, M. coelodonta Muster & Steiner, 2015 and M. lentipes Muster & Komposch, 2015) were formally described, and a new key to all Alpine Megabunus harvestmen was published. Furthermore, by using ecological niche models and multivariate genetic analyses, new insights in the Pleistocene history could be gained. The population structure and the niche models through multiple time-scales showed evidence for inner-Alpine survival on nunataks, and also revealed refugia in massifs the refuge. These results indicate that the Pleistocene glaciations played a key role in speciation by isolating lineages in small refugia. Additionally, this project will form the basis to define protection measures for these cold-adapted species, which are in high risk of being endangered by climate warming.